The last boss is dumb, and breaks like every rule that all of the other ships have established. I really love FTL overall, but designers can be wrong, and I give that design decision exactly zero respect. I imagine were Patrick here he would say the last boss was a design decision and he respects that, but fuck that. It forces you to take each ship (which starts out unique) and basically warp it to a particular playstyle by the time you reach the end of Sector 8. I agree about the flagship being a bitch that requires a pretty specific loadout. I'll probably play some Isaac while I'm at it. And now I'm going to try again, so damn you all. I can get to sector 8 consistently on easy and fairly consistently on normal (using a good ship, like the Red Tail), but I cannot for the life of me beat the rebel flagship. the last boss in FTL is a bitch and requires such a specific loadout to defeat.
