The problem with the Enterprise being under water (for me..anyway) is it's never really explained why it is there, we just have to accept that it's just..well..under water. Why not simply be in orbit like any other mission? Why risk exposing a primitive society to an advanced technological achievement like the Enterprise? There are tons of questions, but I guess in the end we just have to accept the fact is was there for a cool shot of the Enterprise coming out from an ocean.
What is actually shocking is I THINK JJ Abrams was trying to show Kirk didn't actually know what he was doing. He WAS underqualified for his position and needed more training. It's just, without Pike, he needs Spock and his crew to reign him in.