I've seen the film twice, and just watched the bluray, but I haven't listened to the commentary yet, but I was wondering: in the first quarter of the film, Bones is overly worried about Kirk's health. Could this be an abandoned plot line that would have Kirk being relieved of duty because of his mental state?
It's supposed to play into the notions of conflict being set up early on, and indicate that his state of mind is probably not what it should be to take on the mission. It's something that he slowly sheds as they get closer to the mission at hand.