I'm glad somebody else has brought up that TWoK sort of feels at odds with Trek despite being the best of the films. However, I say it is still the best Trek movie because:
It focuses on the characters who know from Star Trek, and their growth, change, loss, and acceptance is critical to the story. While the things that happen to them aren't limited to Trek characters, Kirk, Spock, et al. were the definition of "Star Trek" at the time.
The militaristic aspects aren't totally foreign to Star Trek. While exploration was always at the forefront of their mission, Starfleet was (as Carol Marcus pointed out) still a military organization. What has happened is that the exploration/scientific aspects in the story have been initially shifted to Dr. Marcus.
The sci-fi aspects and story telling are still very strong, it's just that Kirk and Khan shooting each other in a nebula is so great that we forget they're there.
- What are the ramifications of a device like Genesis, which puts a civilization even closer to the ability to "play god?" Is every tool that can create also doomed to be a weapon that can destroy?
- How does a future society balance the often competing goals of scientific exploration with military power, especially given something like Genesis?
- What responsibilities do we have when we decide to "play god" within a much smaller microcosm such as Khan's people. Kirk presumed he was doing the right and just thing by setting them up on a planet but never returned to check on them. Was he responsible for what happened to Khan as a result?
The increased breathing room of a full motion picture that doesn't have to delve into the backgrounds of the characters we already know gives the story room to breath, and unlike TOS we have time to let events that aren't driven strictly by the "gimmick" of the scifi aspect intermingle and impact with the plot device(s).
I still hold that TMP is the most "Trek" of the movies, but TWoK is the best of the movies while still being sufficiently "Trek."
I stand by my head canon that Galaxy class ships are equipped to deposit saucers on planets to establish starter colonies. It's already basically a floating city in space.