I enjoyed Into Darkness, but it cannot be analyzed closely without it being ruined. Also, everyone knowing Khan is in it before release wasn't a mistake, how could it be when they were trying to keep it secret the whole time?
I think there is some worthwhile material in the movie such as exploring the use of drone weapons, and breaking borders in order to hunt terrorists, breaking orders when the law and morality call for it, and the validity of executing in the field rather than going to trial. The problem with the movie is, it starts those interesting threads but goes absolutely no where with them, and does nothing to explore why one action is better than the other. That's the point where it starts getting into the 9/11-is-an-inside-job conspiracy world and things are falling apart by that point.
Shoehorning in Khan as the villain could have worked with smarter writers, but the movie gets bogged down in not knowing what it really is about. When it gets to the point where we have to decide who is the better person, Kirk or Khan, we are left with Kirk being leader of the Enterprise for the same reasons Khan claims he should lead, because Kirk is better than everyone else, just like Pike claims for no apparent reason. We are left with Kirk being the better person simply because he defends the friends we just happen to sympathize with more, so it is really a tribal conflict where no party is morally superior in reasoning or actions.