Fanboys pick out a handful of annoying things that rub against the traditions of the comics, but that is some pretty minor stuff compared to how much they got right and how much they improved on.
I would hardly call re-designing the origin story so that it can be wrapped up at the end of the movie a "handful of annoying things that rub against the traditions of the comics".
Were it not Batman, I could understand the need to tie up the arc. Pick a standard "hero" origin. He is created in tragedy by the act of a criminal. Criminal drives him to become crime fighter. Hero captures criminal, and can rest.
But a KEY and CRITICAL part of the Batman mythos is that Bruce never gets that closure. He never has the satisfaction of finding and punishing Jack Napier in the comics, and TDK did a good job of incorporating recent comic book mythos into the move. While Napier is killed (in BB), it was not at his hands.
So if you ask me, Burton REALLY screwed the pooch on that one by removing Batmans raison d'etre by not only turning Jack Napier into the Joker, but then having him killed at the end. After all, now Bruce can rest, as he's avenged his parents, and his torment is relieved.
Maybe good story telling for a non batman movie, but it makes ZERO sense in the context of the film.
With ALL of that said, and my overall lack of overwhelmishness for the first movie, I completely grant it that it changed the superhero movie genre. It reinvigorated it, redefined it, and set it on the path it rides high on today. And for that I'm thankful.
Oh, and Kim Bassinger was the worst casting choice ever for that role. I realize she was a last minute replacement, but bad acting, bad writing, and prom dresses do not make for a good femme fatale. sorry.