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J.J. Abrams Talks Star Trek 2; Says Filming Begins Thursday and 3D Tests on First Star Trek Convinced Him to Post-Convert Sequel
by Christina Radish (from Collider.com)
He also says that the 3D "was something that the studio wanted to do, and I didn’t want to do it." Ah. He goes on:

And then, when I saw the first movie converted in sections, I thought that it actually looked really cool. So, I was okay with their doing it, as long as I could shoot the movie the way I wanted to, in anamorphic film, and then let them convert it. So, those who want to see it in 3D, which looked pretty cool, can do it, and those that want to see it in 2D can do that too

So 2D is his preferred format, I'd say. He also talks about the casting of Benedict Cumberbatch and other bits and bobs like that.