I have nothing against post-conversion 3D other than "what I've heard." I saw Harry Potters 5-6 in 3D (the ten minutes of each film that were converted) and never saw a problem with it. And I caught the last Narnia film in 3D by accident. It didn't look great, but it wasn't bad either. As for shooting in 3D, Avatar looked great in either format (although I did end up needing to see it flat just to reassure myself that it was in fact a movie I had seen and not some kind of animation).
In general though, my attitude is "see it however the director wanted." JJ is fond of shooting anamorphic, and has cited that has his reason for not shooting 3D (I don't know enough about 3D filming to be aware that the two formats are mutually exclusive, however I take his word for it). As I happen to like his cinematic style, and think it is just what ST has needed, my preference will be in 2D.
On the other hand, it's ST. Unlike most movies, I probably will see this more than enough times to justify one or two trips to the IMAX. And cynically, I have no doubt in my mind that the one theater in town with an 'actual' IMAX screen will choose to project a 3D print of the film.