Yeah, I saw an article somewhere that pointed out what I believe is the problem with the endgame. In the last sector, the feel of the game changes completely. You've just spent seven sectors fleeing before the might of the unstoppable rebel fleet, and you finally get to the Federation base, and they say "OK, now find the biggest, baddest rebel ship and kill it." This jarring shift, combined with the flagship breaking all the rules (e.g. having drones after you've killed their drone systems) and yet still being trivial to defeat using specific gimmicks, really breaks the endgame for experienced players. Like the author of the aforementioned article that I can't seem to find, I only play the first seven sectors now. The final sector is so unenjoyable that I just quit when I get to the final sector and start a new game so I can go back to having fun.
"OK, now find the biggest, baddest rebel ship and kill it. We'll give you fuel and repair your ship, but won't give you any missiles, drone schemas, extra crew, drone parts, or extra weapons". I get the gameplay reasons for most of that, but they could at least restock your consumables.
I even tried to fly through the sector in reverse to see if I could do something weird like assaulting the rebel homeworld. Not a thing you can actually do.
Honestly, an Ender Wiggin moment would actually have been pretty good here. Instead of fighting any of the rebel ships, your goal is to survive until you can jump past each, and when you get to the flagship, survive until you can fire the Super Secret Win Button weapon.
