1. Batman's Voice: The voice that Bale used when he was talking as Batman to Rachel in the Batcave was something that I would have preferred for him to use throughout the entire trilogy.
2. Different Fighting Style for Batman: I think I would have preferred seeing Batman use a different fighting style, something that would have given a better impression that he was more than an average brawler and could do some acrobatic stuff/moves.
3. Personally, I would have had someone else other than Maggie or Katie play Rachel; hell, Kate Beckinsale would have been a better choice. And instead of making her the object of both Harvey and Bruce's affections, I would have given Harvey a wife, where she was pregnant and was killed pregnant, hence adding more reasoning to Dent's line about where his "family" died. I would have still killed off Rachel, only it would have happened later on, possibly in the climax with Joker, where Bruce would really be feeling the raw emotions of anger and we would get to see on how Bruce still overcame that temptation of killing the Joker right then and there when his emotions were still very raw.
4. I would have had Talia reveal herself much earlier on in TDKR to both Bruce and Gotham. I would have had Bane having a separate agenda from Talia, along with Bane having been the actual person to have climbed out of the pit. Talia's motive would have been to clean Gotham out of its corrupted people while Bane would have been planing to take over the entire country, with Gotham as his starting point.
5. To reinforce on how the wealthy were in power while the poor were still suffering, despite crime being at a all time low, I would have probably had Gotham be more militaristic where people were being forced to live by a very strict and harsh law as a result of both Dent's death and how the city felt that by being more harsh with their punishments and laws that it would prevent people from resorting to committing crimes, hence the lower society growing a grudge at the high and powerful.
6. Less time on orphanage, and more time on Selina's reaction to the Marshal Law in the city along with the reactions of its citizens to both Dent's secret and the state of the city.
I could go on actually, but those will do for now.haha