Two things: A, the finale is really idiotic and I can see why John Davison knocked the game for it in his GamePro review.
Isn't this a problem in all of Bioware's games though?
That said, I fucking hate the fuel system. It makes no sense in terms of the codex stuff and forces me to waste money to get places. Plus, if there is a fuel efficiency upgrade, I haven't seen it, and I've gotten every ship upgrade you can get before picking up Jack.