3. Logic
The teaser trailer showed us the Enterprise rising from the depths of the ocean. We have never seen the ship do that before and it made you wonder what it was doing there? Did it have something to do with John Harrison? Is it going to crash in to the water like it was hinted at in the trailer? Well, it turns out that during the mission to stop the volcano from erupting, the decision was taken to hide the Enterprise under water. And considering the planet is full of primitive, spear throwing aliens, you do have wonder why they didnt just leave the ship in orbit. Why would you need to hide it under water? Who can detect the ship in orbit but cant detect it in water? What this tells us is that logical decisions are also not going to play a big part in Star Trek Into Darkness. You can picture the brainstorming session where ideas like Spock in a volcano and Enterprise under water were suggested and enthusiastically incorporated into the script because it would look cool. Thats fine but if it makes no sense then you are setting yourself up for a major fall.