J.J. Abrams has done his duty in giving new life to the dormant Star Trek franchise with two solid films. The next film is already in the works and could hit theaters as early as 2016 but J.J. is going to be busy doing a little indie film at the time. Even though J.J. will have a lot to do with the film (producing, maybe writing, certainly developing the story) someone else is going to have to direct and, it seems, J.J. has someone he'd like to see do it: Ruper Wyatt who is directing Rise of the Planet of the Apes.
Abrams, in an interview with the folks at HitFix, said of Wyatt, "he's incredibly talented and we'd be lucky to have someone as talented as Rupert." This, along with previous rumors of Wyatt's involvement give us an idea that, at the very least, he's being considered. As with all this: wait and see and breathe in and out.