The Dark Knight was a perfect movie, with two minor caveats.
While the Joker recieved exceptional development and a fitting conclusion (one can simply assume that he is locked up in a maximum security prison), harvey dent/two face was not explored fully as a character.
The transition from Dent to Two Face was far too rapid. In the comic books, dent had a history of psychiatric problems that were confidential and thus unknown to anyone before he ever became two face. It made sense that he could go mad. But in the movie, it portrays a strong willed character, who just because the person he loved dies, abandons all logic and goes completely mad. That's not realistic character progression. A person doesn't simply go from sane to insane in an instant.
Two Face needs to come back in Batman 3. It makes perfect sense that Two Face was locked away at Arkham Asylam by Gordon without anyone's knowledge. If anyone found out that dent went crazy, the entire mob that was prosecuted by Dent could go free. Batman didn't check his pulse, he had no way to be sure that Dent was dead. There was no body shown at the memorial for Dent. So it makes perfect sense that Gordon would have gotten Dent the help he needs in Arkham while letting everyone think Dent is dead.
By bringing Dent back, introducing initially as a psych patient at Arkham, Nolan gets a chance to mention his confidential past where he did suffer from schizophrenia or multiple personality disorder with psychotic breaks.
Also Two Face is way too intersting and way too important a charater in the batman mythos to have been killed off in less than a half hour. There is a lot of room in Two Faces development. In one two face story arc, he develops a third personality unknown to the first two, that of justice, to right all the wrongs in the world. That would make for a great story arc. Two Faces existence becoming known, the mob getting retrials only to be hunted by two face's third personality - justice, and batman and possibly even two face getting retribution would all make for a compelling story in the third film.
Lastly, it seemed to me that in Batman Begins the league of assasins actual motivation for destroying was barely touched upon. This wasn't a big issue, as the league of shadows is no where near as major a part of the batman mythos as two face, but a bit more emphasis on the fact that they are essentially terrorists, who oppose technological progress or who wish to rid the world of all it's filth, and destroy the cities that are corrupt beyond repair, would have been good. If the league of shadows was to make a return in Batman 3, with their motivation further explored, it would make for a very fitting conclusion to the trilogy, and would make for a fantastic trilogy. Even ignoring the league of shadows entirely, and instead simply delving deeper into the Two Face storyline in the third film, would make for the greatest trilogy of all time, bar none.