I thought that had to do with BB taking place mostly in the "barrows" (I think that's what everyone referred to that area as...the slums of Gotham).
Begins rarely ventured away from the slums, so we only got to see the gritty Gotham of that movie. Then in TDK, since the movie took place outside of the "barrows" or whatever it was called, probably in the middle and upperclass districts of Gotham, this time we got a "cleaner" looking Gotham.
There was a scene in Begins (right after Batman takes down the gangsters loading the stuffed bears filled with drugs near the trailers) where Batman is standing on the roof of a skyscrapper and the scene pans out to show the cityscape of Gotham, and for that one moment, BB's Gotham looked exactly like TDK's Gotham. I think it just had to do with which part of Gotham BB focused on.