Things I didn't like:
1. The lens flare. My god man, what was he thinking? I know everyone has mentioned this, but damn, sometimes it was unbelievable how in the way it was.
2. McCoy with his "Damnit Jim!" lines. I think one time would've been sufficient, but I'm pretty sure I counted at least three occurrences of that line. I started to feel like it was being shoved in our face. "Look, they're the same characters as before...see". Scotty's one line near the end was the only one that really seemed to fit.
3. Chekov's accent interfering with the voice recognition. It just so happen to be on the same letter as vessel (as in nuclear vessel) too. I always thought that thing was coded to your voice, so this one seemed doubly lame to me.
4. Kirk making out with the green alien chick. Yeah, I know he did that a lot in TOS, but again, it seemed forced. It seemed like just another "Hey, remember, Kirk makes out with green aliens". I also always thought he only did that because they were in deep space and there wasn't anything else around.
5. Sulu forgets to take off the "parking brake". I know most of this is suppose to show that they're inexperienced, but again, it was a groaning moment for me, especially after Pike asked if he had done it.
6. Kirk gets a captains commission and the Enterprise at the end. I get that he was getting an officers commission for his actions, but to go straight to captain and get the flagship starship? Again it just seemed a little overdone to me. Maybe someone else with a military background can sound off on the accuracy of that. It obviously had to happen, just seemed like a "wow" over the top moment.
Other than those things, I liked it a lot. It was probably better than all the prequels combined too.