I don't really like the way they have done the final boss.
It's not (only) because he's difficult, or because the RNG can easily fuck you over (although that contributes a fair bit), but because learning how to effectively fight him is tedious.
You make an error or the RNG hates you - restart the game, play through all the sectors again, new fight against the boss, screw it up again, wash, rinse, repeat...
I know that the ironman, rogue-like-ish nature of the game doesn't leave many options there, but still...
Given it's the final fight and by far the most difficult, too, it would be nice to have some way to repair a bit during phases, or some kind of second chance at the fight if you screw up (at some cost).
Maybe some store to do some (limited) swapping of equipment if you end up with a sub-optimal loadout.
Or some single-use specials you can collect in the game that will then grant some temporary boost to your ship.
Edit: And what's worse, with AE he has gotten even more dangerous, esp in phase 3. I can make it through the first two just fine most of the time, but he always most of the time wrecks me within a few minutes.
The supershields (which sometimes recharge) mean you need a lot of firepower to reach his systems while he does massive damage to me and his mind control is trolling me.
Also the rebel fleet is taking control of sector 8 much too fast, imho - I can barely visit one or two special beacons (repair or the very, very rare store) before I have to reach the base to fight the boss.