We'd expect J.J. Abrams to know better than to do something like converting Star Trek 2 to 3D post-shooting. As the elected emperor of the film nerds, we'd expect Abrams to embrace the mentality about 3D: it should generally be reserved for films shot and visualized in the medium. A lot of movies opt to apply 3D post-shooting as what is widely considered a cheap ploy; 3D rarely contributes much to the moviegoing experience here. Then there are films like Avatar and Hugo, which were conceived and shot in 3D, and show in contrast how the technique can actually enhance the story and the world within the movie.
To Abrams' credit, he seems to be taking a very thoughtful stance on the conversion, telling MTV that the production team will employ a "a good high-end conversion," and that they "have the months needed to do it right."
But this isn't all the news surrounding the format of the upcoming Star Trek sequel. Abrams has also made mention of shooting the movie in IMAX, although he seemed less assured that this endeavor would take place (despite his apparent passion for IMAX).
All of that aside, Abrams offers a good deal of confidence about Star Trek 2: "The three writers, Damon [Lindelof], Bob [Orci] and Alex [Kurtzman], wrote the most amazing script. And I am thrilled to get a chance to direct it. It's totally mine to screw up. So if you don't like it, [it's] completely on me. Our sets are almost done, so we go back and start shooting next month." This 3D thing might be a slight rift in your usual good judgment, Abrams, but I think we're all still pretty pumped for the Star Trek sequel.