I think the plus side for JJ is that he can write/direct good action scenes with some nice drama thrown in occassionally, engaging characters, and keep stuff moving at a fast pace. One of the downsides with his work on ALIAS, and from what I heard about Lost is that his stuff can sometimes fall under the weight of its own complexity or convulted storylines.
With Trek, I think he will craft a pretty good action film with just enough emotion to elevate it above mindless. But I doubt that it will be deep or profound sci-fi, or tackling any social issues. It will be a feel-good popcorn movie designed to appeal to the largest number of people possible-which has pluses and minuses I suppose.
At first I was pissed at the whole redoing Kirk and Spock thing that I heard Abrams will do. But now I look at like who cares? It doesn't erase the 40 years of previously established Trek, on screen, comics, cartoons, or books. And even if it does, it doesn't mean that I have to go along with that. I like what I like.
I'll give Abrams's film a chance because I liked the early years of ALIAS and I thought MI3 was a blast. But I'm not expecting much.