My major gripes were:
Bonzo's death was really underwhelming
Valentine wasn't portrayed importantly enough
Peter wasn't portrayed evil enough
They cut out the Locke/Demosthenes thing, which isn't a huge deal, but it would have been nice if they included it
Petra seemed too much like a romantic interest, she's really supposed to be a substitute Valentine
The battle school game (the one for which the book/movie is named, by the way) wasn't very well done at all, they really should have followed it exactly like it is in the book, they changed the rules and it wasn't very good. They made it so you didn't need to have 5 players to win, which is why you couldn't just cheat the way Ender did, kinda making his genius underwhelming.