Honestly I could write an essay about what worked and didn't work with the film, but I doubt anyone would read it.
Stuff I didn't like
-Bruce Wayne, too much of a bafoon. The playboy image is fine, but he should still be competent and not an embarassment to his families legacy.
-Lack of Detective skills, this is true for all Batman films though
-Gadgets- still hate the tumbler, the bat cycle in the tumbler and the bat call in his boots
-Batvoice and poor fighting sequences
Stuff I did like
-Supporting cast is stellar Oldman, Caine (they didn't give him enough for the second film), Ledger, Neeson, Murphy, Eckhart, Batmanuel..... Really they stole the show every time.
-Alfred, again, in the first film he was a very important part of the plot, he's a paternal figure for Bruce and really brings an emotional depth to the film that wouldn't be present otherwise. The alfred's of past films were okay, but the films would have been the same if they didn't have them in it at all, this is not true for Nolan's films.
-Big action sequences, the fighting may have sucked but some of the other stuff is really great. Like the motorcycle semi scene from movie #2.
-I've hated the realism argument from day one (it's a movie about a billionaire crime fighter, that throws realism out the window) but the stories took themselves seriously and worked. I still think they would have worked on their own without being a batman film though.
-I'll say it again, the supporting players. The characters had depth and you really came to feel for them. The actors just played the parts well. I think Eckhart was amazing as Harvey Dent in movie #2, really an overlooked performance by most people I think. Scarecrow worked because Murphy brought this level of creepiness to it.
So basically the stuff I didn't like really centers around the Batman character himself and Bale. I think he's a talented actor but for whatever reason I don't we've gotten the best out of him for these movies. The third film is really looking to fix some of the issues, and it certainly seems to push Batman front and center.