Hey guys, just saw the movie and I thought it was fantastic. Just wanted to throw out a few things Bob Orci said over at Trek Movie since I saw everyone discussing them.
The Enterprise underwater- Basically the interference from the erupting Volcano would not allow them to transport without direct line of sight and they couldn't get close enough with shuttlecraft without risking being seen.
Khan's blood being uses instead of another cryo sleeper. Basically, Bones wasn't going to risk killing another cryo sleeper, since the unfreezing process was tricky, when there was still a chance they could get Khan. Also, he had no idea that anyone's blood other than Khan's would work since he has seen what happened with the tribble. Since Kirk was on ice time wasn't really of the essence, they had a chance to let things play out.
Also, the blood itself did not just save Kirk. It was a starting point for a serum that Bones created to reverse the radiation damage by restoring the cells. They had to make sure he wasn't still iradiated after the procedure.
Now, I would like to speculate on Khan's appearance. Since he was working for Section 31 and they value their secrecy and planning, I would assume that he was forced to undergo plastic surgery to fit in with his new cover identity. It really is the only logical conclusion I can come up with. Thanks for reading.