It's been mentioned a ton of times on this thread, but the alternate takes being used instead of ones from the various trailers and TV spots were really puzzling. The biggest omission for me was the Joker with his back to the camera, slowing walking toward the Batpod (with that ever so slight limp), drawing his knife. The take Nolan used was from the front, and the effect was greatly diminished. How do they not put such an iconic shot in the finished film?
but there were some fantastic shots and takes of dialogue that should've been used.