the change of aesthetic style between BB and TDK has a lot to do with the story. Directors (good ones, anyway) don't say "lets make this look dirty!!!11!" unless there's a logical reason; one that visually sells the mood of the story.
BB was dirty, and somewhat stylized to help show how awful the state of the city was; how desperate it was for a hero. TDK was cleaned up and less stylized to not only show how much Batman had helped, but to also add weight to the terror that Joker was causing. If the Joker was causing all that mayhem to a downtrodden city like in BB, it wouldn't be nearly as effective.
The city and overall art direction of TDKR will depend on where Nolan is taking the story. Obviously, Batman being on the run will be a major factor of the plot, and I think that psychological consequences of that will be symbolized with a return to something similar to BB. I also don't see, nor like, the idea of red being this movie's "theme". Red symbolizes anger, war, and blood shed, but (simply looking at it from Batman's perspective) won't be his angle. Not to mention red is a terrible color for film, and hardly ever occurs naturally, so it won't make sense to have that be the hue of the flick. I think a greenish color might be best, or hell, coming full circle and going back to a brown/golden color like in BB.
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