There wasn't much that I didn't like about The Dark Knight some of which has been stated already and maybe some not so obvious to others:
-The Tumbler (Bruce should have built a car)
-Bale's Batvoice (I agree that its too intense but maybe being a young Batman he modifies it over time)
-Gordon choosing his son over his daughter (not sure why this bugs me)
-Harvey dying (why must villians die in superhero movies?, at least Joker was captured at the end)
-Batman becoming a true viligante at the end of movie. The city hates him and the police can't openly work with him now. Its like it undid all the work he started in Begins and through the start of The Dark Knight.