The What, Why & How-to of Favorite Ships

[xdesperado]

Okay this thread is a place to talk about our favorite ships.
Yes I know there have been several other threads about favorite ships but this one will be a bit different.
How so you ask? Well the answer is that this isn't just a simple listing of ships. But why they are our favorites and how we set them up with upgrades and use them.
Obviously different people will have different favorites and the type of captains they play and their style will make a difference in choices of ships and how they upgrade them.

I hope that by creating this thread we can help others to better understand the possabilities and methods that have been proven to work and avoid some of the mistakes we have made.
Also it may prove an incentive to try new and different ships and styles of play.

[xdesperado]

Index to Ship Write-Ups

Inquisition Cruiser by xdesperado

Hyper Freighter by xdesperado

Omega Cruiser by Fenikso

Serpent's Tooth by Fenikso

Tempus Fugit by johndramey

Hyper Freighter additional ideas by bruceasinger

Pirate Skylift by xdesperado

SlayerNZ Cruiser by athios

Serpent's Tooth additional ideas by xdesperado

Tempus Fugit additional ideas by absimiliard

[xdesperado]

Would ask that submissions to this thread follow this basic outline for ease of reference.

Ship Name and basic statistics before upgrades

Brief description of why its a favorite and intended use.

Upgrades added and why they were chosen along with options or special upgrade notes.

Finalized Ship stats after upgrades

Notes on your play style, more indepth look at how you use the ship, and other relevant information.

[xdesperado]

Notes on Upgrading Ships
The most important thing to remember about upgrading ships is that once an upgrade is installed there is no going back or changing it.
As long as you own that ship it will have the upgrade you just installed so make sure it's the right one, or at least one you will get a real benefit from during the life cycle of that ship.
Upgrades can extend the usefulness of a ship, such as your starting ship.
Help overcome design weaknesses, like a lack of Cargo Space or Torpedoes.
Or create specialized ships that are very good for specific roles, like Exploration, Spy Battles or all out Combat.

Having a plan for how you intend to use the ship will help you pick the right upgrades.
Also keep in mind the ships starting strengths and weaknesses. Certain weaknesses can be compensated for or overcome with upgrades. Other limitations are inherent to the design of that ship and can't be overcome with upgrades. A fast, quick ship with 80 crew and 20 cargo will never be a good ship for trading, its too W-F hungry and can't carry enough goods to make it practical. That same ship on the other hand could be very good for assassination/bounty hunting contracts in early to mid game with proper upgrades.

Additionally remember that not all upgrades are created equal. Do you really want to settle for Battle Prow's +4 Armor, because its all that's currently available or that you can afford, or do you want to hold out for Dreadnought Architecture's +6.
Knowing the benefits and in some cases detriments of the various upgrades will allow you to make better choices.
Also keep in mind that sometimes the "penalties" of a given upgrade can be made to work in your favor.
If your looking towards making some cash and earn some XP as a privateer/pirate then an upgrade that increases chances of encounters becomes a benefit, while still being a serious detriment to a trader or smuggler that wants to be left alone.

Finally remember there is such a thing as "too much of a good thing". If your ship already has Hull 40, Armor 20 and Guns 40 do you really need or want more armor or guns? Likewise if your crew is already 225 will adding more actually prove useful or just create problems and make the ship less efficient.

[johndramey]

Very good idea for a thread, I have a ship that I want to write up so I'll put a placeholder here and fill it in when I got some time.

I'll be writing up the Vegas Class when I find the time.

[xdesperado]

Inquisition Cruiser
Hull 16
Armor 15
Engines 33
Sails 38
Crew 120
Cargo 95
Guns 30
Torps 21
Speed Fast
Agility Quick

Its a well rounded combat ship right out of the dock. Speed and agility makes it deadly at any range. Enough crew to have the advantage in numbers over the vast majority of ships with only Omega Cruiser and some Alien ships being able to match its performance with a larger crew size.

Contract work, assassination, bounty hunting and blockades are its primary use. Secondary use is Privateer/Piracy.

Upgrades
Structural - Cargo Hold
Apply this upgrade last to get maximum benefit from it.
While not a total W-F hog like some ships, its never going to win any prizes for econemy. You'll want all the cargo space you can get to carry essentials like W-F and weapons while leaving room for some loot.
This ship is a dancer and not a slugger. While it's fairly tough it will never stand up in a slugfest with larger hull vessels, so extra armor doesn't add much to it.
Extra engines are a slim possability but since its already got a good E-H ratio they aren't really justified.
The ship has almost too many guns for effective Privateering already. Adding more just means your more likely to destroy a target before you can loot it.

Combat - Escape Shuttle or Weapons Locker
Escape Shuttle for when it all goes wrong as sometimes happens. Better to lose your favorite ship than your favorite captain.
If you prefer a combination Gun Bunny/Boarding style or straight Boarding style then the Weapons Locker is a viable option to the escape shuttle. Allows room for more W-F, Weapons and Loot.

Interior - Advanced Bridge System or Water-Fuel Tank.
Advanced Bridge System to help you dance rings around other ships, even Fast/Quick ones with higher level captains.
Alternatively the Water-Fuel Tank allows for really long contracts even deep into red sectors.
Don't add crew upgrades as they have a dramatic impact on your W-F useage and require much higher skill levels to utilize effectively. 120 crew means you out man most ships anyways. If you don't, then use your agility and guns to trim their numbers down or kill their engines before boarding.

Propulsion System - Titan Components or Advanced Sails
Titan Components give bonuses to all your combat actions from medium range and closer. Helps you dance around those really high level enemies and rip them to shreds with your guns.
Advanced Sails for those who prefer missiles and aren't as worried about looting the enemy.

Armament - Cargo Pod or Predator Tracking Array or Torpedo Control Pods.
I play mainly as a Military Officer Gun Bunny/Boarding style captain so the extra cargo space gets my vote.
If your not a MO or Bounty Hunter then the Predator Tracking Array is a must have for doing Assassination/Bounty contracts.
If you prefer Missile combat then the Missile Control Pods probably offer your best bet for maximum efficency there.

My Upgraded Inquisition Cruiser
Hull 16
Armor 15
Engines 38 (Titan Components)
Sails 38
Crew 120
Cargo 126 (Cargo Pod + Cargo Hold)
Guns 30
Torps 21
Speed Fast
Agility Quick
Additional upgrades - Escape Shuttle and Advanced Bridge.

As I mentioned above, I play mainly a Military Officer Captain with a combination Gun Bunny/Boarding style. If I can't get a quick clean engine destroyed victory then I'll start alternating between targeting engines and targeting decks. Once I feel I have a decisive edge in numbers, or if because of missplaced shots I fear the target might be destroyed, then I go for boarding.
Note this isn't a ship for low level captains as you'll need some pretty good skills in Piloting, Tactics and Intimidate to get the most out of it and not have it be a W-F hog. At a minimum I'd suggest 30+ Pilot and 15+ for Tactics and Intimidation. If your ever going to engage in boarding actions then 15+ Warrior is also called for. Below those skill levels and it will be too much ship to handle. With that said if you have the chance to buy one early go ahead and just keep it in dry dock until your skills are up to the task.

[xdesperado]

Hyper Freighter
Hull 24
Armor 6
Engines 26
Sails 48
Crew 49
Hold 188
Guns 20
Torps 4
Speed Fast
Agility Medium

Spy Battles, Trading and Smuggling. Can't beat the cargo capacity and with its small crew is very W-F efficient. The fast speed helps cut down on encounters and aids in escaping them when they occur.

Structural - Cargo Hold
This isn't a combat vessel. Trying to make it one is a waste of time. You got it for its cargo capacity so maximize it. Depending on other upgrades added you may want to install this upgrade last.
Explorers might find the Ancient Reactors bonus for wilderness exploration a possible option, but its hard to justify giving up 37 extra cargo, especially since the small crew severely limits its usefulness in exploration.

Combat - Escape Shuttle
Really no other options here, at least for me. Eventually your probably going to get caught in an encounter you can't escape from and your limited combat abilities won't be enough to win the fight.
I suppose dedicated smugglers might find the Weapons Cabinet or Artifact Isolation Chamber an alternative so they can cram a little more in, but its asking for trouble in my opinion.

Interior - Water Fuel Tank
With good Pilot and Intimidate skills you can go from one corner of the Quadrant to the oppisite corner on 25 water. Means the rest of that lovely cargo space can be filled with other things. Plus it helps reduce signature which is a bonus.

Propulsion - Advanced Sail System or Cargo Pods.
Advanced Sail System reduces encounters and will help you escape when they occur.
Cargo Pods increase your already large cargo space but will also increase your signature so they will raise your risk factor.
Spybank is an interesting alternative but is only useful for Electronics so may get under utilized.
Smuggler's Hold is the final option if you plan to do Transport and Message contracts in addition to hauling cargo.

Armament - Omni-Stealth Array or Cargo Pod
Omni-Stealth Array helps turn you into a giant hole in space making this a great Spy Ship and helping to insure you reach your destination with all that cargo.
Cargo Pod is just like the Propulsion upgrade with the same benefits and drawbacks.

My Upgraded Hyper Freighter
Hull 24
Armor 6
Engines 26
Sails 60 (Advanced Sail System)
Crew 49
Cargo 225+25W-F (Cargo Hold & Water Fuel Tank)
Guns 20
Torps 4
Speed Fast
Agility Medium
Additional Upgrades - Escape Shuttle & Omni-Stealth Array

I love Spy Battles and this is my ship of choice to use for them.The W-F tank means I can get to my target sector and back to a friendly port again after spending enough time to collect the full 225 Records the ship can hold. Looking to build Rep in a hurry or make friends with a former enemy this will do it. Also makes for easy XP and nice boost to the bank balance. Your stealth upgrades mean you'll get very few encounters and thanks to the Sails you'll be able to avoid or escape most of the ones you do get.
Also can't beat it for making a killing on ending shortages.
Just remember its limitations in combat and don't grow to attached to it. Sooner or later you'll likely run into a high level enemy with a real combat vessel who you just can't shake. When that happens use the Escape Shuttle before its to late. You'll most times have made back your investment in this ship several times over, so just go find youself a new one.
Because of the small crew size you can fly this ship effectively at a relatively low level. Pilot 24+, Tactics and Intimidate 10+ should be enough to see you getting good results. If your Captain is more into trading and smuggling than combat, building up your Stealth skill can further enhance the stealthy nature of this ship.

[slayernz]

Hey Xdesp, I made up a quick table that you could slot in for the purposes of easier comparisons between the stock ship and the pimp-my-ride ship.
Here is the rough and ready Excel spreadsheet that you can use to convert into the proboards table format. It's ugly but it works.
ShipTable.xlsx (11.02 KB)



Example:
Inquisition Cruiser

Attribute	Stock	Modified	Comments
Hull	16	16
Armor	15	15
Engines	33	38	Titan Components
Sails	38	38
Crew	120	120
Cargo	95	126	Cargo Pod+Cargo Hold
Guns	30	30
Torps	21	21
Speed	Fast	Fast
Agility	Quick	Quick
Other			Escape Shuttle, Adv Bridge

Hyper Freighter

Attribute	Stock	Modified	Comments
Hull	24	24
Armor	6	6
Engines	26	26
Sails	48	60	Advanced Sail System
Crew	49	49
Cargo	188	225+25WF	Cargo Hold+WF Tank
Guns	20	20
Torps	4	4
Speed	Fast	Fast
Agility	Medium	Medium
Other			Escape Shuttle, Omni-Stealth Array

[xdesperado]

slayernz thanks for the tables.
Unfortunately I can't access your file or create similar tables on my cell phone...and I don't have a computer.

[Fenikso]

Omega Cruiser

Attribute	Stock	Modified	Comments
Hull	15	15
Armor	15	20	Hyperion Superstructure
Engines	33	38	Titan Components
Sails	38	38
Crew	170	195	Mercenaries
Cargo	90	108+25W	Cargo Hold + Weapon Cabinet
Guns	30	30
Torps	21	21
Speed	Fast	Fast
Agility	Quick	Quick
Other

Fast and Quick combat ship with big cargo and a lots of crew. It is basically an upgrade to Inquisition Cruiser but W-F consumption goes significantly higher. Not recommended for green Captains, but deadly in hands of experienced one. Great for just anything related to combat with Gun-Board strategies. It is also great for opportunist as it will not let you down in any intense situation.

Upgrades
• Cargo Hold – With a big cargo hold +20% cargo hold upgrade makes perfect sense. On Impossible you will need it for all the W-F and rest for Weapons. But also adds versatility for piracy as you can take more loot.
• Weapon Cabinet – Weapons boost for boarding or boarding defense.
• Titan Components – Bonus for combat on medium and short range, +5 extra engines are not really needed.
• Mercenaries – More crew, boarding and combat advantage.
• Hyperion Superstructure – As any Quick / Fast ship it is a bit fragile. Boosting Armor is a good idea for unlucky event of being shot or rammed.

As I play on Impossible and very aggressive combat oriented strategy I want to win every fight. Using Torpedoes / Guns / Boarding seems to be the best and most effective approach to prevail and this ship just supports it well. I usually fill my cargo space with just W-F and Weapons in a ratio which my Captain can handle at the moment. Right now it is 80 Weapons and 53 W-F.

Do not be fooled, this ship is the last on my upgrade chain. I start to use it very late in the game when my Captain is ready.

[Fenikso]

Serpent's Tooth

Attribute	Stock	Modified	Comments
Hull	12	12
Armor	7	11	Hyperion Superstructure
Engines	24	24
Sails	14	14
Crew	40	40
Cargo	30	46+25W+25W-F	Cargo Hold + Weapon Cabinet + Water-Fuel Tank + Cargo Pods
Guns	21	21
Torps	6	6
Speed	Medium	Medium
Agility	Quick	Quick
Other

My most favorite starting ship. I tend to start doing contracts and picking fights early on. I am also big fan of opportunity-piracy as it pays off very well. It is Quick and has a lot of guns so it is best utilized at short range shooting the hell out of merchants and smugglers.

Upgrades
The biggest drawback of the ship on Impossible is the cargo hold as it drinks W-F like crazy. So adding cargo hold upgrades is my priority, the ship has enough of everything else.
• Cargo Hold
• Cargo Pods
• Water-Fuel Tank
• Weapon Cabinet – This is my favorite specialized cargo hold upgrade, as when you carry pirated Weapons you are safer against boarding. I also like to attract trouble and Weapons increase chance of enemy encounter.
• Hyperion Superstructure – For picking fights early on there is no thing like "too much armor".

It fits my overall aggressive strategy. Piracy! Fights! Danger! Trading? No thanks. I usually do some contracts first, buy Trade Permits with my favorite factions and then immediately turn to piracy. Carefully pick some easy fights with merchants or smugglers in faction space early and sell loot. When I can afford a few upgrades and improve my combat skills, I start full front piracy and move to more dangerous sectors as the loot becomes more profitable.

In combat I move to close range as soon as possible and fire my guns on enemy ship's engines. 40 crew armed with some Weapons can protect the ship from boarding attempts but when things go south it is just easier to run like hell.

[johndramey]

Fenikso - Nice posts!

slayernz - Thanks for the excel sheet, I'll be using that!

I'm actually going to be writing up two different ships, so bear with me guys. I'll be putting a write up for the Tempus Fugit here later!

So I found the time and am working on getting some achievments unlocked, so I'll post up my upgrade path for the Tempus Fugit first!

------------------------------------
Tempus Fugit

Attribute	Stock	Modified	Comments
Hull	9	9
Armor	5	5
Engines	18	24	Ancient Reactors
Sails	18	18
Crew	26	26
Cargo	35	35+25	WF Tank
Guns	12	12
Torps	4	16	ARES Class Missile Control
Speed	Fast	Fast
Agility	Quick	Quick
Other			Escape Shuttle, Smuggler's Hold

Why do I like it?
Well, that's a hard one to explain. Usually I think most people skip over the Tempus Fugit because it's relatively lackluster in stats. It's a relatively small ship and pretty low on armor. The only thing that makes it a nice ship to start with is the smuggler's hold but I think that's a bit of a double edged sword. I think most advanced players see that as a reason for not taking the Tempus Fugit, a smuggler's hold is a useless upgrade in terms of combat or trading; it's really only useful for completing delivery contracts. Ah, there we go, the main reason to take this ship is it's early game play style.

With the Tempus Fugit you can easily run around the quadrant doing delivery contracts with relatively little worry. If your reputation is above -5 you can pretty much surrender to all military ships without a second thought. I usually use this little bugger as my super secret starter ship for this reason.

What about the future?
Good question! Like I pointed out above, I think the Tempus Fugit has very little combat or trading promise. "So what good is this stupid thing then?" you might ask. Well, listen up boys and girls, we're going on a little platonic journey. Ask yourself this, what methods are there in the game to build up XP and credits without engaging in trade or combat? None? Really? Think about it a bit..... Spy wars! That's right, we want to kit this bad boy out for spying. We'll keep her in the relatively safe upper "free" zone of the quadrant because, let's face it, she's not good enough for the big leagues yet. She can, with the proper upgrades, become a formidable stealth ship for running contracts, spy wars, and ending small but high priced shortages.

Why the upgrades?
I'll be the first to admit I'm no pro at ST. I pound my head against insane and, 9 times out of 10, die before I hit level 5. What happens to that one magical pilot that survives? Well he usually makes it to at least level 7! So, well, take my upgrade path with a grain of salt please.

Ancient Reactors are chosen because of the bonuses for landing operations and the +6 engines they give. Dual purpose, allows you to land more easily and helps if you do manage to get caught in combat. Retreat!

Escape Shuttle is pretty self-explanatory. We want to avoid combat at all costs, but sometimes you just can't. The shuttle will be there when you need it, just hop in that bad boy and zip to the nearest friendly planet to buy yourself a new ship when necessary!

Water Fuel Tank is not so much for increasing the range of your ship, instead we want to increase our loiter time. How long do you need to hang out in Thulun space and perform surveillance until you find some honor? Hint: A long, long time!

Smuggler's Hold comes standard! Who needs options, anyway? It'll be helpful when you are starting up and if you need to fall back on contracts to get some money!

ARES Class Missile Control is our final option. I tend to keep both my pilot and stealth skills way, way up when running with the Tempus Fugit. This let's me (in theory) sit out at max range and just plink torpedoes at any enemy that I can't run away from outright. Eat hot leaded-torpedoes, coppers!

Play style pointers!
I generally use the Tempus Fugit with the spy class. The reasons should be pretty self evident, but to keep everything clear I'll just point out that she is a beast for early game stealthing. Try to keep your pilot and Stealth skills up around 200% of your level and dump the rest into tactics. Don't start taking part in spy wars until around level 7. By that time I generally have 14 Pilot/Stealth and about 8 or 9 tactics which is typically enough to make a haul on Spy wars. Try to keep 3 or 4 factions happy with you so you have some safe havens to put into when you need to refuel or repair. Go hog wild!

[Fenikso]

johndramey - I am interested! I never had success with that ship. Not sure why.

[bruceasinger]

Jun 19, 2013 17:56:36 GMT -5 xdesperado said:

Hyper Freighter
Hull 24
Armor 6
Engines 26
Sails 48
Crew 49
Hold 188
Guns 20
Torps 4
Speed Fast
Agility Medium

Spy Battles, Trading and Smuggling. Can't beat the cargo capacity and with its small crew is very W-F efficient. The fast speed helps cut down on encounters and aids in escaping them when they occur.

Structural - Cargo Hold
This isn't a combat vessel. Trying to make it one is a waste of time. You got it for its cargo capacity so maximize it. Depending on other upgrades added you may want to install this upgrade last.
Explorers might find the Ancient Reactors bonus for wilderness exploration a possible option, but its hard to justify giving up 37 extra cargo, especially since the small crew severely limits its usefulness in exploration.

Combat - Escape Shuttle
Really no other options here, at least for me. Eventually your probably going to get caught in an encounter you can't escape from and your limited combat abilities won't be enough to win the fight.
I suppose dedicated smugglers might find the Weapons Cabinet or Artifact Isolation Chamber an alternative so they can cram a little more in, but its asking for trouble in my opinion.

Interior - Water Fuel Tank
With good Pilot and Intimidate skills you can go from one corner of the Quadrant to the oppisite corner on 25 water. Means the rest of that lovely cargo space can be filled with other things. Plus it helps reduce signature which is a bonus.

Propulsion - Advanced Sail System or Cargo Pods.
Advanced Sail System reduces encounters and will help you escape when they occur.
Cargo Pods increase your already large cargo space but will also increase your signature so they will raise your risk factor.
Spybank is an interesting alternative but is only useful for Electronics so may get under utilized.
Smuggler's Hold is the final option if you plan to do Transport and Message contracts in addition to hauling cargo.

Armament - Omni-Stealth Array or Cargo Pod
Omni-Stealth Array helps turn you into a giant hole in space making this a great Spy Ship and helping to insure you reach your destination with all that cargo.
Cargo Pod is just like the Propulsion upgrade with the same benefits and drawbacks.

My Upgraded Hyper Freighter
Hull 24
Armor 6
Engines 26
Sails 60 (Advanced Sail System)
Crew 49
Cargo 225+25W-F (Cargo Hold & Water Fuel Tank)
Guns 20
Torps 4
Speed Fast
Agility Medium
Additional Upgrades - Escape Shuttle & Omni-Stealth Array

I love Spy Battles and this is my ship of choice to use for them.The W-F tank means I can get to my target sector and back to a friendly port again after spending enough time to collect the full 225 Records the ship can hold. Looking to build Rep in a hurry or make friends with a former enemy this will do it. Also makes for easy XP and nice boost to the bank balance. Your stealth upgrades mean you'll get very few encounters and thanks to the Sails you'll be able to avoid or escape most of the ones you do get.
Also can't beat it for making a killing on ending shortages.
Just remember its limitations in combat and don't grow to attached to it. Sooner or later you'll likely run into a high level enemy with a real combat vessel who you just can't shake. When that happens use the Escape Shuttle before its to late. You'll most times have made back your investment in this ship several times over, so just go find youself a new one.
Because of the small crew size you can fly this ship effectively at a relatively low level. Pilot 24+, Tactics and Intimidate 10+ should be enough to see you getting good results. If your Captain is more into trading and smuggling than combat, building up your Stealth skill can further enhance the stealthy nature of this ship.

I mostly play merchants with very high stealth {150% of my level}. This is my ship of choice.

In the early part of the game before aliens become common, I go with

Structural - Cargo Hold
xdesperado is right, this is cargo ship, not a combat ship. If you get into close combat with this ship, none of the other structural upgrades will help you win the combat. The best they will do is let you survive a little {maybe} longer. You are still blown up. Up the Cargo and stay out of combat at medium and short range. And long range to if you don't have very high stealth.


Combat - Escape Shuttle
I go with cargo pods, 7 extra cargo. If you have very high stealth, normal ships can't close with you and the Escape shuttle is not needed. Of course, this all change once Aliens become common. Also, if don't keep a very high stealth, then normal ships maybe able to close range with you and if they do and you can't get back to long very quickly, the ship will not last long.

Interior - Water Fuel Tank
I go with the Water Fuel Tank. The other option is Cargo Pods which adds 12 cargo. I always have more than 12 fuel so the extra cargo is only going to be carrying fuel anyway. Plus, it protects me from saying, hey it is only 4 green hexes away plus 1 leave and 1 to land, so I only need 3 fuel, and then have 5 ships interrupt the landing and now my crew is hating me. With the Water Fuel Tank, there is never a reason not to have 25 WF at the start of every journey. And as xdesperado says, it gets you to nearly anywhere on the map as long as your sails don't get damaged.


Propulsion - Advanced Sail System or Cargo Pods.
I always go with the Advanced Sail System (ASS) for two reasons. The ASS takes you from 48 to 60 sails. This helps both your WF use and disengage chances. Somewhere, I remember reading that Cory stated that there were additional bonuses every time you passed a x0 amount. The ASS gets you a 50 and a 60 bonus. The Cargo Pods gives you 10 cargo. But the reduced WF rate and better disengage chance more than makes up for any extra cargo.

Armament - Omni-Stealth Array or Cargo Pod
I go with the ARES upgrade to 16 torps. With my high stealth and 60 sails, I have never had a ship be able to close with me. I can sit out at long range and torp them until my my torps eventually hit. I have only been hit by 3 torps. {Twice in a row from a low level ship with 12 sails. How it hit me once, let alone twice is a mystery to me. Luckily it only had two torps so I don't know if it was some random coincidence or if his tactics was that high} Most ships can't take 16 torps so the adding the ARES makes it deadly against any ship that can't take 16 Torps. And if the ship does somehow take more than 16 torps, say go for you and retreat. I love blowing up and capturing those pirates than turn their prow to me and try to capture me.


With 60 sails and high stealth, the chances of running into a normal ship that has more sails and a higher stealth so it can close with you is almost 0. You are able to stay at long range and retreat whenever you want. You are very safe until you screw up and hit the wrong button.

Now this all changes when Aliens start appearing. From what I read, there is a class of Aliens that have very high stealth and Lots of sails. You may not be able to disengage from them at will. Once Aliens start becoming common, I change my ship setup to the following.

Structural - Cargo Hold
Same as before. None of the other upgrades help much in combat, and Cargo Hold gives you an additional 37 cargo bays. Will be helpful to carry more spice.

Combat - Escape Shuttle
Eventually, you are going to encounter a fast Alien ship that has higher stealth and more sails than you and you won't be able to run away from them. You are not going to win any combat with them so your best bet is to escape in your Escape Shuttle.

Interior - Water Fuel Tank
I go with Advanced Bridge System. It gives you Pilot and combat bonuses. It doesn't specifically mention stealth bonus, I believe it does so I get it to help improve my chance to disengage.

Propulsion - Advanced Sail System or Cargo Pods.
Again I go with Advanced Sail System. Those extra sails may be what allows you to retreat for those aliens. Plus "Provides a bonus in deep space for avoiding encounters."

Armament - Omni-Stealth Array or Cargo Pod
The Omni-Stealth Array says it "Major bonus for moving in deep space without encounters."
The other option is Sail Command Probe. It gives you 4 more sails that helps in disengaging. It also gives you pilot bonuses which hopefully includes stealth. And it gives "This command probe increases the manuverability of the ship in deep space."

Currently, I am going with the Omni-Stealth Array because "Major bonus for moving in deep space without encounters" sounds like it significantly reduces the chance of encounters with Aliens which is most likely better than adding a small chance to disengage from combat. Now with my high stealth and high sails, the disengage bonus of the command probe might change my chances of disengaging from the alien from very likely to almost always and be a better upgrade for me. I have now way of testing this so I am going with the options that "Sounds" better.

[xdesperado]

Pirate Skylift
Hull 14
Armor 9
Engines 24
Sails 24
Crew 40
Hold 70
Guns 24
Torps 2
Speed Medium
Agility Medium

If Cory Trese told me I could pick any ship to start a new game with, this would be my choice. It's small enough that even a starting Captain won't get eaten alive by W-F consumption. Tough enough to handle the types of encounters you'll have early game with the firepower to make short work of the enemy. Has enough Hold space to make it a legitimate trader or support exploration, spy battles and blockades. With upgrades it can retain its usefulness much longer than any of the starting ships and upgrading it for a specific role can keep it useful until quite late in the game. Basically its sheer versatility makes it hard to beat in the early game.

Upgrades
Part of what makes this such a special ship for me is that its basic stats can support a wide variety of upgrades allowing you to either have a solid general purpose ship or a tightly focused specialist.
Because of this for some Upgrade locations I'll recommend what not to install and why.

Structural - Any except Structural Refit and Battle Prow.
You have better options for adding more armor that will either enhance its combat abilities or give you a bigger boost in armor.

Combat - Any
That said I'm not a fan of most of the boarding upgrades and given the limited crew size, even adding upgrades to crew won't make this a straight boarding style ship long term.

Interior - Any except Additional Crew Quarters or Exo-Planetary Crawler.
You have much better options for adding crew and if you are planning to use this ship for exploration additional crew will probably be much more useful than the Crawler.

Propulsion - Any except Extended Mainsails and Prow Sails.
You have better sail options that will take you above the 2-1 sail to hull ratio mark.
Note; the Water-Fuel Recycling Plant is probably not a good option either since the ship is pretty efficient anyways and has a good Hold size.

Armament - Any except the Prow Lance Battery or Torpedo Control Pods.
The big weakness for the Pirate Skylift is only having 2 Torps. Neither the Prow Lance Battery nor Torpedo Control Pods do enough to make it a viable Torpedo range combatant. If your Cadar or just enjoy Torpedo combat install the ARES Class Missile Control. The Aft Lance Battery is a viable option for those looking for a few extra Torps to help discourage pursuit.

My Basic All-arounder/raider
Hull 14
Armor 9
Engines 29 (Titan Components)
Sails 24
Crew 55 (External Crew Pod)
Hold 96 (Cargo Prow & External Crew Pod)
Guns 24
Torps 16 (ARES Class Missile Control)
Speed Medium
Agility Medium (Quick)
Additional Upgrades - Escape Shuttle

This combination increases the combat effectiveness at all ranges and allows plenty of room for loot in addition to your W-F and weapons.
If I'm feeling especially aggressive and brave I'll install the Weapon Cabinet and Shalun Mercenaries instead of the Escape Shuttle and External Crew Pod.