Breathe a sigh of relief. Cinematographer of Batman Begins and The Dark Knight Wally Pfister has no intentions on using a 3-D format in the (still unannounced, but seriously how can it not happen) third installment of the Nolan/Bale Batman franchise.
Pfister actually was very adamant about not shooting in what he calls the "3-D fad" claiming that the format might have worn off by the time the movie is released. He does leave the option of shooting at least some of the film in IMAX, just like the infamous bank robbery scene from The Dark Knight, which for anyone who saw that sequence you know that is good news.
What is known for sure at this point, according to Pfister, is that Bats 3 is going to happen and it will be shot old school on film. Right now there is a tentative release date of sometime in 2012, but seeing as the film is in no farther than pre-preproduction that time frame could easily change.