Something I dislike about nuTrek: it tends to undermine the potential for the characters to realize their development when the materials for showing it is built into the plot. It stands out more in STID, which is really a more complex story with more moving parts. In particular, the dialogue fumbles with Kirk's maturation and with the Enterprise's mission.
In the first case, Kirk faces four moments in which decides to act in impulsive ways: saving the planet, trusting Marcus, trusting Khan, and finally, sacrificing himself. In spite of the disciplinary measures, the first time works out. The next two times are complete disasters. Because of his cumulative decision making, Kirk is placed in a position in which the only person he can really turn to is he himself. I found the scene moving: Kirk's life reduced to kicking a piece a machinery. It was pathetic, worthy of Sisyphus. However, there was no follow through. There's no reflection on what he went through. there was nothing on par with "I feel young" to acknowledge his own transformation.
The second case concerns the nature of Starfleet. I feel that Scotty gets unfairly taken to task for voicing his objections to the torpedoes and to the mission in general. Nonetheless, Scotty's and Spock's objections ended up sounding silly because they were forced in arguing a false dichotomy: is/isn't SF a military organization. How did both become so simple minded? Why didn't they present a more measured response to the mission? Hadn't they just acted in a humanitarian and anthropological capacity in saving the Nibirians? Indeed, Kirk fumbles himself when describing the ethical side of SF. I'm not sure that old Kirk would not have taken the opportunity to describe what would have been lost had the Nibirians been destroyed (Picard certainly would do so). Kirk probably would have dismissed Spock and Scotty if they tried to bring up the Nibirians in context, but that would give some indication of Kirk's state of mind (perhaps explain his decisions with regards to Marcus and Khan). It seems strange that these people could not be more sophisticated when dealing with their purpose.
I don't think that these problems are major: like I said, the raw materials to deal with them are in place. And I think that character development could have been dealt with through a few lines of dialogue, not changing the plot radically or making the film seem stolid. Nonetheless, more self-reflection and sophistication would make the film more emotionally and intellectually satisfying.