If you have ship designer, why don't you use it instead of buying flagships
Flagship is very nice to have, but it is better to design your own specialized ship.
Your build as it is is completely terrible against aliens.
While you can get away with junk stats like Explorer or Negotiation against normal ships, against aliens having 20 junk points spent away is a suicide. Your only lifesaver is your huge warrior that you gained by sacrificing tactics.
Here are few comparisons between normal ships and Aliens:
Normal ships are only up to 190% your captain level. Aliens are up to 200% + your difficulty's percentage level. Meaning on impossible they can reach up to 390% per level, even though they are EXTREMELY RARE!!! (My highest so far is 310% of captain's level)
Alien builds are more likely to be more specialized for boarding.
Alien builds are more likely to have higher warrior than you.
Aliens are the grim reapers here sent by the Great RNG. They tell you when your time is up (in a sandbox game it sounds a bit weird, I know, but you know, when the RandomNumberGoddess decides, you have to go... There are a couple of ways you can defy death, but more on that below)
If you want to deal with aliens, it is much better that everyone is on good terms with you. Because aliens themselves are going to bring huge trouble upon you, especially with the captain level that limits your build on a couple of aspects.
I dare to say, I'm a successful alien hunter and even though my runs always end in a misfortune (one was killed while he was on holiday - which taught me to ALWAYS fly in my battleship once I have one, but most of them are rammed by pirates... However, NONE OF THEM were killed in a legit fight against the aliens; Torping builds unfortunately are doomed against aliens due to RNG rolling them a closing in turn and then another one). And I have experimented quite a bit with stuff on the run too.
So, as you could already see, there are two ways you can defeat aliens. The simpler one is torping, the more complicated one is boarding. Each one has its' own advantages and disadvantages and I'm about to break them down here. And no, you can't deal with higher level aliens consistently with guns, because during a boarding attempt the attacker's main stat is warrior and the defender's main stat is pilot. So if you meet an alien 300% your level with enough warrior, you are pretty sure to lose the boarding roll... And cannot retreat, because your tactics skill is too low.
Torping is a simple hi-stealth and low-Pilot build. The more stealth you have, the merrier (but you still need some tactics if you want your torps to land), because the key of torpers is to maintain long range and mash the torp button. You also have to use a fast ship with lots of torpedoes, because aliens have like 50 hull and sometimes even 40 torpedoes might not be enough against them. Since they don't rely on boarding at all, they have more freedom of choice of officers, but I choose a Veteran, because he boosts torping against aliens, then I pick a pilot and mechanic... Because a mechanic prevents solar sails damage from solar hazards, while pilot helps a little with fuel consumption and also avoids radiation storms. If you don't feel you need that, you can pick a third officer according to your liking, but I would say the mechanic is a must, because in order to find aliens, you need to use artifacts and not a few of them... I carry 30 or 40 artifacts with me. Not only it boosts Veteran's powers, but also attracts aliens... Especially the more powerful ones, hehe
According to the guide there are several alien AI types, but in my career of an alien hunter I've noticed no difference whatsoever. Only Narvidian hunters sometimes like to use torpedoes and from time to time someone wanted to gun me, but the vast majority wanted to close in range and board. Which helps the torpers in their survival, since Alien ships are only normal speed, so closing in might be very difficult for them, but the RNG can screw us over nevertheless even with Stealth 250% of our level.
According to the guide the aliens also receive crew bonuses based on how many artifacts are you holding on your cargo... But they are completely irrelevant, because if they board us, we are pretty much dead anyway.
As mentioned, first stat is Stealth. Second stat the torpers need to raise is tactics. You don't need to raise pilot much, since the fuel consumption isn't going to be an issue, since we need only enough crew to keep the ship running, not as much crew as possible, like in case of boarding. So you can raise it a little, I do it to 10-20, but then I leave it static. The rest is junk stats.
Advantages/Disadvantages of a torping build
+ You can do it indefinitely, as long as the RNG doesn't roll you two close-ins. Then you're dead.
+ Huge stealth allows you to always Ignore in the worst case. And oftentimes you can retreat if you find the alien too deadly to your liking, for example huge alien level.
+ Huge money from alien hunting
+ You're probably a Cadar. If not, you're doing something wrong, like choosing a wrong starting faction. It is very important to be a cadar with a cadar ship, because if you have a ship from your own faction, you have some nice stuff
+ They are not as vulnerable to factions hating you, because as mentioned above, you can escape many unfavorable encounters. It is still better to have all factions like you, because it's easier to find a planet where you can repair and refuel your ship.
+ hitting the patrol button is faster than trolling over one square and you can see more easily when the alien rumor burns off
- If you run out of torpedoes, you need to retreat. Do NOT EVER try to close in to mid range and use guns, that's suicide. On mid range pilot matters much more than stealth, except for range gaining actions.
Now let's talk about the boarding class. The boarding class is the sole reason why you should NOT wage two wars, which is a war against aliens and a war against factions. Because it is very vulnerable due to highly specialized build.
The thing is, this is all a decently prepared boarding alien hunter needs for hunting aliens. Decent crew, huge warrior (the more, the merrier), huge ship that is at least MEDIUM/MEDIUM (sure, you can go for low/low, but... It's not the best idea to say the least.)
However, having huge warrior skill means you need to sacrifice other skills for it. How huge warrior do you need? Well, I'll give you a brief description of the skill.
Pilot - cuts down fuel consumption - not too relevant, since our consumption will always be huge - and helps with maneuvering against guns and is the main stat that resists board
Explorer - exploring planets. Irrelevant in battle.
Negotiation - Cuts down buy prices, increases sale prices, and helps with morale increase during mutiny if you bribe your crew. Irrelevant in battle.
Tactics - Help with success of a blockade/surveillance, targeting guns and torpedoes (having 12 tactics on lv 31 renders your 40 torpedoes useless btw.), also are an essential stat if you want to retreat from being boarded. However, it is less relevant than warrior in boarding action unless you're using the Board-run strategy, which is unadvised against aliens. I have read that with passing tome the blockades and surveillances are easier to perform anyway, so this stat could maybe be needed only around the 12.
Stealth - helps you avoid encounters, retreat from them, maintain long range or retreat to there. Also helps in reducing of ship damage from board and hit rate of torpedoes. Nobody in the whole game has enough torpedoes to cause any trouble, and damage isn't that hard to repair, so this stat is irrelevant for us. Even if they do have enough torpedoes, the AI will not allow it. That's how RNG works in our favor for once.
Warrior - Increase damage done by crew by boarding and being boarded, chance for a successful board and increases your chances to hurt the enemy captain in a duel
Intimidate - Reduces fuel consumption, reduces the crew morale decline when you run out of fuel (if you have for example 6 intimidate, you can maintain 4 crew without water-fuel. For 10 crew you need around 12 intimidate or so) and reduces the crew morale damage it receives in battle. Intimidate is important to keep the crew fuel efficient in space, but with enough warrior the crew morale damage is already well protected, so intimidate is unnecessary.
Of course the equations in this game are more complicated, but basically warrior is the most important skill in both boarding and giving damage while boarding, so you need huge warrior... I use some tactics for having easier blockades and surveillances (a good source of exp) and some for pilot...
Because unless you pour pretty much every stat into warrior, you need a boost in warrior. I use warrior 200% of captain's skill and Leviathan upgrade, so I have nice warrior, however this is not enough anymore. Pre-v6 strength used to not be counted towards level, so you could have strength 300% of your level without problems, effectively negating and even overpowering most alien strengths (since they still have a cap). However, as the strength is now counted into the level, it is no longer possible unless you pour every stat point into warrior.
So you need a boost and this boost is gained from your cargo and officers... However, the officer boosts are so irrelevant that at the beginning you don't really need them with huge warrior (later on they might be more relevant, but none of my captains lived long enough to tell the story... My record is lv 71). But weapons are very relevant, because each weapon gives you a boost of 3 warrior. So for example 80 weapons give 240 warrior and so on. This, however, attracts the attention of enemy bounty hunters/warships for illegal cargo and pirates... Well, pirates will hunt you even with water-fuel. If you have a huge warrior, bounty hunters and warships pose no challenge, but pirates and their annoying ramming!!! This has costed many lives of my alien hunters, because the pilot skill that protects from ram wasn't high enough.
This is also the reason why you shouldn't wage two wars. Because you can easily raise your pilot to defend against the pirates' ram... But then your warrior is hurt, which means you are relying on weapons more. However, weapons give you a static boost of 3 warrior per weapon. In practice it means that 80 weapons will give a huge boost of warrior until you reach 240 warrior... From there it begins giving diminishing returns until weapons become so irrelevant you might as well drop them.
This means two things...
Even alien hunting isn't possible forever. One day, unless the pirates pick you off by ramming, you will meet an alien that is stronger than you and will kill you, because weapons simply aren't so strong anymore.
If you get stronger against aliens, you are weakening yourself against pirates' ram and they love ramming a lot. However, you can't even surrender to those pirates, because if your reputation is below -50, they will execute you!
Which is why I told you to get upgrades to reduce encounters... Because you cannot wage these two wars as a boarder. You will eventually be killed by an alien or a pirate.
If you have all friendly factions, the only problem are independent pirates. Surrendering to them will loot all your hard earned weapons, so you have to fight... And again eventually die by being rammed. However, before that happens, you can have so much fun waging war on aliens. Much more fun than dealing with pesky faction ships that are weak and easy to dominate. So I suggest you to get at peace with everyone, up the difficulty a bit and go hunt some aliens
This problem of ramming pirates has several solutions. I have built several funny builds for alien hunting, which shouldn't be taken seriously, but can be real fun to play.
1. Ramming speed!
The purpose of this is simply to destroy ships by ramming. You will receive no rewards from it and may eventually ram your ship instead of the enemy ship, but if you have escape shuttle, it will not bother you. This build pushes every possible point into pilot, earning money through peaceful quests and merchandise and then spending it all on ramming damage fixes. It is a troll build, but can be a great deal of fun, because with a pilot officer, reinforced prow, pilot boosting upgrades and a fast/quick ship (but with lots of hull and armor) you can challenge even highest level alien ships (since ramming comes BEFORE boarding). And you can pay back to both aliens for those mercilessly killed captains and indy pirates too, how sweet is that
2. No weapons!
The principle of this build is maximizing warrior. Up there I have said that you need some pilot to avoid being rammed by pirates... This build will omit having any weapons. But in exchange it pumps as much as possible into Warrior. Screw pilot, screw tactics, screw them all! Boost warrior, get a Leviathan, you'll need it, and hit them hard!
I have this build reinforced by the fact that whenever I surrender to a pirate, they will never steal any water-fuel from me. So the only losses I have is one morale hit and one hp hit. Not that significant.
If you maximize your warrior and get a leviathan, you should in theory be able to challenge even the highest level aliens, ecause your strength is more than 300% your level, warrior is the same and leviathan will give you huge warrior boosts. You can also completely throw away the bodyguard, because you won't need captain damage soaking from board, and take the vet just for the money and when you have enough money, you can dump him for someone insignificant, like a spy.
This build has one huge advantage compared to regular warrior build. Water-fuel is cheap and it can be done indefinitely, since the only thing in play are character skills.
But back to our normal warrior build. Our normal warrior build, at least at the beginning, relies on his weapons boost to give him the edge. I have already tried fights against aliens without weapons and I need to say, if I met an alien that was 350% of my level and he had high warrior, I would die. So weapons are a necessity.
As for the upgrades, it is more complicated here.
The best ship is a ship with as much cargo as possible and as much crew as possible, as little hull as possible to save fuel, 40 sails and 36 engines and as little amount of weapons as possible. I use Steel songs as boarders, because their 160 crew can give me a boost of 80 crew with Battleship architecture. It is a custom designed and a very expensive ship though.
Truth is though, at the beginning it isn't absolutely necessary, because even on impossible difficulty the crew losses aren't that huge. So some fuel can be saved by not buying this upgrade. However, do this only with huge warrior.
Other than that, the upgrades for a boarding alien hunter are pretty much fixed.
Dreadnought architecture is a must with reinforced prow being the only alternative if you want resistance against ramming.
Crew xeno suits for lower warrior guys, on higher warrior leviathan is better and on higher level, as weapons are fading off, leviathan becomes a must to keep the warrior up (because you need to deal damage to the enemy captain, otherwise the tides can turn and damage will be dealt to you!)
For an alien hunter a null field generator would be a must.
And of course, for an alien hunter the omni stealth array would be junk, since we want to meet aliens... So hyperion superstructure.
advantages and disadvantages of being a boarding class:
+ boarding isn't influenced by RNG too much
+ multiple ways to build the character based on your expectations
+ the progress is pretty stable
+ not bound by guns or torpedoes
- very expensive at times
- lifespan influenced by ramming pirates. Of course you can buy an escape shuttle instead of leviathan, but you'll need huge warrior for that and huge crew... Or you can try the funny builds
- patrolling is inefficient. Instead it is better to just move in and out of the square with alien rumors.
- cannot be done forever
It may look weird that these things really work... But they do. That is because the aliens have to spend so much exp on strength too that the other stats, earlier important, like tactics for keeping track of huge crews during boarding, and things like that... needed to e sacrificed by the aliens too so that the warrior could be maintained.