I also want to know why the Enterprise
can get to Qo'Nos and back faster than I can get from DC to Manhattan, and why that barren rock McCoy and Marcus landed on had breathable atmosphere, and why Chekov could beam a free-falling Kirk and Sulu and cancel their velocity in ST09
, but couldn't beam Khan up here. I'd also like to know why Carol Marcus wasn't killed by running while beaming.
These are my own personal explanations.
1) The Enterprise and most Starfleet ships have been equipped with transwarp, or something similar. This could be because transwarp has become common after Voyager's discovery of it, and the Narada took it back in time.
2) I don't have a strong explanation for the atmosphere
but I don't see why the Enterprise doesn't have some atmosphere magic or why the planetoid they were on couldn't have a breathable atmosphere, like so many places the crews of the Enterprise have visited.
3) For the beaming, it was said that there's too much interference to beam Khan. Is that a thorough explanation? No, but it's vague enough to work for me so that's fine. Plus beaming in the new movies seems to allow people to move while beaming compared to previously. In the first movie Spock could move and reach out for his mother, and Amanda Grayson's fall even cancelled out her beaming. I actually like this, it shows more strongly that the beaming is a continuous shift and the person on both ends are the same. It lessens the frightening argument that beaming creates new people (although does not eliminate it completely).
With magic tech like transporting I don't think cancelling velocities would be too hard.