Well, I went and saw it again this weekend and in 2D. Much better the second time around.
The first time, in 3D, I was a bit overwhelmed by all the action and it was hard to track. I think it took a little but away from the human element, which was much stronger in 2D. I was more engaged with the characters this time, my old friends that they are, and the character arcs worked better for me. The action also made more sense. Mostly. While brighter, the set piece at the downed saucer was still hard to follow at times. And how did it suddenly become night?
It's one of the features of modern action movies, it seems, that the human frame is subject to impact trauma that should have resulted in more injuries. It's mostly Kirk who suffers from this, being thrown into a bulkhead by Krall, and then hitting that huge rock after Jaylah releases him. I deal with these sort of things professionally and they really should tone it down a bit. James T. Kirk may be a hero, but he's not a superhero.
Likewise Bones was a little too much over the top at times, though I love Karl Urban. I would like to see more softer Bones moments, where we see the soft heart under the crankiness. We do see that, I just want more. Also, the wound to Spock was in his torso, not his "iliac region" which would be lower and closer to his hip.
All that said, I'm giving it an A-. I left the theater in a jolly, positive mood and had the usual heightened visual sense of my surroundings – which is always a sign to me that I have seen a good movie.
Bring on the next one!