He does ensemble casts the best, and he can work in humor while still making it a dramatic show. But I am not sure how good he is really with exploration of typical science fiction themes. It would probably also be action- and character-focused. Which aren't bad focuses, but maybe not... "Trek" enough sometimes.
I think JJ didn't make that bad a job either. The problem is that he needs to learn how to avoid writing giant holes. Or rather, care about not writing in such holes. Lense Flare and Shakey Cam all work for me just fine, and so did the characters. I dislike that he had too many plot holes and inconsistencies in ST XI.
I sure hope you are wearing flame retardant clothing. I think most would agree that Rick Berman and Brannon Braga was the death of Star Trek (pre-JJ Abrams). If Uwe Boll directed a movie, he'd seal the coffin shut for good, and throw away the key. No thanks.
I liked Abrams approach, myself. While it is good for the series to be thought provoking, you also have to remember that it's a movie. It's gotta have some action in it, otherwise why not just make it a TV serial? Plus, he just created a new continuity, he needed the entire film to estabhlish the characters introductions, what changed in their backstories, the villain and how he connects to the characters... I think he did good with what he has.
Another director for me would probably be Joss Wheadon, he's done some pretty good Sci-fi, and his brand of techno babble actually makes sense! :p