Another issue that I have with warp drive in Nu Trek is how they don't seem to have multiple warp speeds. For example, in STID Kirk and crew seemed blown away that someone could have caught up to them while in warp. I guess they never heard of any warp speeds faster than...what, 1? As I recall in the prime universe, Kirk's Enterprise could go warp 7 safely. In TNG it was 9. A better way to have that part of the movie go is for Kirk to order them back to Earth at Warp 7 or something. Then when the Vengeance catches them they could have just been shocked that it could go at warp 8 or 9 since that would have been clearly beyond their technological capability (again, in the prime universe anyway).
Of course there's the whole transwarp idea but that's never really clearly explained in the movie and they continually refer to their faster than light speeds as warp, not transwarp. So yeah, I suppose transwarp is the best theory it just sucks that it's not more clearly explained in the film. The only trans anything that gets talked about is the beaming.
So yeah...that part of the movie kind of bugged me.