Here's the thing with the Dark Knight. I really like the movie, but I think that quite honestly, if you cut the last 40 minutes out, and ended it with batman standing over the destroyed ruins with Rachel dead, it would be an absolute, bonafide great movie. It would take extreme balls to do this, and I understand why they didn't go that way, but I think you have a perfect 2 hour batman/joker film in there, and then instead of a perfect ending, we suddenly restart and its like a two-face short-film attached to the end.
I don't buy Harvey-Dent's transition, they do as much as possible to set it up throughout the movie, but there simply isn't enough time because they're trying to do too much, and as a result I don't really buy the turning point hospital scene.
I also really, really don't buy the Ferry sequence. The first half of the movie works so hard at being grounded and realistic, yet this whole situation just comes out of no-where, and its incredibly contrived. How did the joker get all those explosive barrels on those Ferry's un-noticed? Why is Gordon stupid enough to decide to move all the prisoners? He gives a half-assed justification that makes no sense. You're worried the Joker might try to break them out, so instead of leaving them in the highly secured prison, lets start transporting all of them to god-knows where, even though the Joker just ambushed a prison transport literally yesterday.
The cell-phone bat-vision system kind of arrives out of no-where. I think its a stupid thing to introduce in the first place, and while I like that they address the privacy issues of it, batman is breaking so many laws already, you have to wonder why he wouldn't just keep that thing around. The movie is basically saying "Well, it's ok to wiretap the city, as long as we just do it this one time", and I don't know that I buy that argument. Either don't use it to begin with, or keep it running so you can stop the next villain from coming along.
I do really like the final scene with Gordon/Batman/2-face, I think it works really well, and is a quite powerful, I just feel like it would work better as the end of a 3rd batman movie that was a sequel to Dark Knight.
Also, someone brought up how the Dark Knight basically endorses the ideas/policies of the Neo-cons. I agree, but I actually have zero problem with that, because the entire idea of a vigilante super-hero like Batman is inherently Neo-con, so I think its very unfair to criticize the movie for political reasons. Conservative values make good action/adventure stories (see most of the 80s/90s action classics), that's an inherent fact, so I don't think its an issue.