While I love the movie, two things stood out to me while watching it again last night.
One, when the Enterprise is knocked out of warp by the Vengeance, nobody mentions they are near Earth. Then, in the climax, they're falling into Earth's atmosphere out of nowhere.
Second, Khan is underused. Cumberbatch is fantastic, and great at showing how brutal Khan can be, but we don't get to see his great ruler side. Throwing in a Shakespeare quote during the climax would have been a nice nod to the original Khan.
Also, Khan didn't have a plot other than saving his crew. I feel like they set him up for a return in Star Trek 3. But with these rumors that he will be in the new Star Wars movie might mean that's not in the cards.