I think the differences between the first and second Star Trek movie mirror some of the same issues that I have with the second Transformers compared to the first. The first Transformers is cocky and stupid but manages to carry me through the movie without to many questions and contain certain scenes and set pieces that are satisfying and well made. The second ones (Into Darkness & Revenge of the Fallen) are more confusing, less satisfying and overall a lot worse to experience.

Specifically, the opening sequence in Into Darkness is a god damn mess.
They (Spock and Kirk) are on a planet they are not allowed to be on, doing something they should not be doing, while also arguing with each other like it was someone other than themselves that are responsible for the situation they are in.

All of the arguing results in both defying each other in ways which goes against the person they where at the end of the first film (Kirk goes from learning to be a leader, to acting like a kindergarten teacher around crazy kids. Spock goes from having learnt how to express his feelings and having earned a friend, to yelling at that friend and sacrificing his own life for a mission he does not agree with). All of this for putting a bomb in a volcano and saving some aliens lives. Something that could very easily have been done from outside the planets atmosphere.

The movie could just have started with Kirk being relieved of his duties as captain while arguing about how the mission was handled. We don't need to, or want to see it.