Hmm so between now and 2016 (Trek's 50th anniversary) JJ is supposed to direct and produce, Star Wars VII, Star Trek XIII, and Mission Impossible 5, and any other movie and TV projects he aspires to complete....
The man is an artist. Not a director for hire. He'll give 2 years to Star Wars, take a break , and maybe focus on other projects. Paramount will likely ask JJ to be a consulting producer for Star Trek XIII. Since JJ dragged his feet about even saying he would commit to Trek sequel back in 2011 while promoting Super 8. However I think Paramount will go a different route and choose another director to helm Trek. It'll be like the Bond franchise almost.