I friggin hated that movie! Man where do I start?
Well the first thing that comes to mind is how Batman makes himself known to the general public. Now I'm no comic book reader and I could be wrong on this, but to me, Batman has always been a mystery to the general public, and not someone who shows up to a public court hearing in full costume.
I also agree that two face was way way way way off. The Riddler was messed up also, again I could be wrong on this, but to me the Riddler was always kind of a behind the scenes villian, not someone who robs banks and acts crazy. To me the Riddler should be calm and cool, like a person who thinks they have all the answers. Robin seemed to old to me, and what is up with the Batcave being seperated from Wayne Manor by a simple wooden door. And did anyone else notice that when the alarm was sounded in the cave, you know "intruder allert", that instead of everything being locked down, it becomes exposed, the car and everything. The whole two girlfriends thing for two face was a novel idea, but I thought it sucked on screen.
There are more, but I'll give it a rest for now.