Maurice Navidad wrote:
Kirk comes to realize Mitchell's changes endanger his ship, ergo Mitchell and must be marooned
Elisabeth Dehner's name is the one missing in this phrase.
I agree with a lot of what you wrote, and it's true that Hollywood blockbusters tend to shy away from this simple story technique, resulting in too many films never surpassing their by-the-numbers scripting.
For instance, two recent movies that I really wanted to like, Green Lantern and Captain America, suffer exactly the problem you describe. Cap's only 'problem' throughout the movie is 'will he get the girl?', or 'will he stop the Skull?'. Despite losing his best friend Bucky, we never get the feeling Cap paid a price, or that he had to overcome a personal price or shortcoming before the end of the movie...
So despite a healthy budget, capable direction and a recognizable protagonist, Captain America failed to reach beyond a mediocre premise and story execution.
Green Lantern fares even worse. I saw both films at about the same time, and my memory of GL is even murkier than Cap. Not a good sign...