Must ... not ... derail .... although in saying that I have ONE Steel Song captain in my roster (Captian Glurk the Stoopid).
I must confess in Impossible, I have had reasonably good success (one in five captains make it to level 20, but most of those captains go on to at least level 50 then to 100), but that is because
I do NOT hunt Xenos in Impossible. I never board enemy ships until I have killed their engines and/or they have surrendered. I focus on Pilot first, Pilot second, and ... yeah, that's about it. You need to have some tactics to be able to be more accurate in combat (at least that's what I remember in my captain's basic training lessons). "Only increase tactics when you start missing". Investing in Stealth allows you to avoid encounters, but if you have a good ship and high pilot (with a spritzer of Tactics), you should be golden. Orbiting above a Steel Song planet, with multiple strobe lights, RF emitters, and a trail of Steel Song debris is more beneficial than running silent.
Pilot at 2+ times your level will keep you alive.
Now in saying all of that, you're after specific advice on how to deal with Xenos, especially in mid-late stage games.
First up on levels. The whole adage of an enemy captain = 190% of your level in impossible is true. Does this mean you should avoid adding any XP to your captain to artificially keep your captain level low? Myeahmaybedependsnotreallykindasortano. Don't forget that there are two parts to the game difficulty. One is the enemy captains = 190% of your level, but the other part is that the game becomes more difficult as time goes by. You mentioned this already so do know about it. The difference isn't that dramatic though and the formula is pretty straight forward:
Formula for calculating turn difficulty is as follows:
INT ( Turn / (200+5xDifficulty Level) )
As Cory's mentioned in other posts, the difficulty level is a bit backwards.
Impossible = 0
Insane = 1
...
Basic = 7
SO that means at turn 1000 (about 3 years in), the game level is 4 for most levels, but 5 for Impossible.
At turn 10,000 Basic is at level 42, Crazy is level 47, and Impossible is level 50.
Balance your captain's level to try and at least keep up with the game turn level, otherwise you'll find that even basic things will give you grief.
So back to what you need to do. Boost your Warrior and Intimidate to at least your captain level - if not a smidgen higher. Of course it means you are investing in:
Physical Stats:
* Quickness
* Strength
Trained Skills
* Pilot
* Warrior
* Intimidate
with a blurp towards Stealth and Tactics.
Get some officers. THe ones to use are the Alien hunter, the Pilot, and then either the Military officer or the Veteran officer.
Ship upgrades should include
Structure
* Dreadnought Architecture
Combat
* Leviathan System OR Escape shuttle. If you have unlocked Star Paragon, consider the Crew Xeno Suit or Hyperion Exo-Suit, but bear in mind the latter only boosts the captain.
Interior
* Mercenaries
Propulsion
* Don't really care
Armament
* Predator Xeno Torp array or Hyperion Superstructure
Escape shuttles are extremely useful when you're about to get hull breached with the Xeno, but if you are focusing on boarding, then flag it.
Finally, carry Weapons - I don't remember ever seeing a post saying they lose effectiveness in the long game, however I don't board and I don't Xeno hunt, so I could be wrong
Carry some artifacts too, as they are the aphrodisiac of choice when trying to ensnare a Xeno lover.
Fly in red zones - away from the green shipping lanes. Alternatively orbit dead planets and do your thang.
Good luck - you're a braver captain than I am and I hope that you will live to level 30.