The Dark Knight by a fair ways.
Although it had flaws of its own (like trying to cram Two-face in at the end there), it gave alot more effort to its build up and being a singular cohesive story.
Begins wasn't bad, but was cluttered. Sticking the origin story in eats up tons of time, and the whole final act felt a little rushed as a result (This applies a lot to superhero movies in general).
The Dark Knight rises was a cluttered mess that showed apparently no one learned a thing from Forever and B&R, because they suddenly try and shove 4 new major characters in at once. Predictably, the cohesiveness and development of everyone suffers, and existing characters (like Fox and Gordon) are almost shoved out of the movie (Heck, even Batman was fairly minimal) On top of that, after forging some success with alternative takes, they suddenly bend over backwards to make nods to the comics, which all prettymuch seemed heavily shoe-horned in.