The only real change that needed to be made was to make it an actual sequel to The Dark Knight, instead of just another sequel to Batman Begins. Seriously. A few tweaks made with Rachel and Harvey (Perhaps having Rachel die in the first movie due to Scarecrows toxin or something be the reason behind the 'Dent Act' and getting the criminals off the streets) and its like DK didn't happen at all. I get the reason behind it, not wanting to mention Joker at all out of respect for Heath (though its pretty fucking dumb reasoning - how does it show respect to totally ignore one of his best performances?) but that kind of real world meddling didn't help.
For specifics... As someone else mentioned, change the whole thing about his wounds. At first, I thought that was all a cover. Like he was using someone elses charts as an excuse for why he was a recluse, but apparently its real? That would only make sense if he had still been Batman for those eight years. But its made clear throughout the movie that he hadn't. Also, we see that he has a lot more scars on his body - that he wouldn't have gotten as a result from Dark Knight, which again, doesn't make sense if he hasn't been Batman since then.
The ending. I actually believed that Nolan was gonna do it. It felt right. Despite how lame it was that the climax was reduced to 'bomb with ticking clock' (are we really still doing that shit?), the impact of killing him off would have made up for it. And yeah, even if they aren't going to kill him off, at least make it ambiguous. This is Nolan, he's very fond of oblique endings (Memento, Prestige, Inception all have them), so have Alfred nod at the camera, cut to black, roll credits. Woulda worked.
Sure, I enjoyed the film. There is enough in there to explain away most of the plot holes (if you pay attention, and can hear over the bad sound mix), but its only a three star movie, lets be honest.