Abrams claims that in order for the movie to be made he had to agree the film would be in 3D because Paramount Pictures wouldn't release a non-3D movie. Originally Abrams said he would prefer to not do 3D but it was announced shortly after that Star Trek Into Darkness would be filmed in 2D and post-converted to 3D.
"The studio said, ‘You have to make it in 3D if you’re going to make it, for economic reasons.’ But my feeling was I didn’t like 3D. So the idea of doing Star Trek in 3D was ridiculous. But that was very helpful in some ways, because it let us work with stereographers and the 3D crew in a way that didn’t assume we just loved 3D."
Stuff like this will lead to the further spiral of Hollywood, imo. The artists don't even have the freedom to create anymore.