I also think there is an extremely heavy subtext of physcology.
Kirk demostrates some extremely strong traits of narcissim.
SPock display strong traits of Autism spectrum disorders.
While Khan is clearly a Psychopath.
Kirk is shown directly on screen to be an indescriminate womanizer. He clearly treats woman like objects. He has no regard for federation protocols and directly expresses the opinion that he is above the law because he gets results. While detractors would sugguest this is because he's written as an immature child, to advance a superficial ADD plot I think its to blatant for that to be true.
From the beginning core Characters such as Pike, Spock, and Uhora are seen objecting to his ways. The fact that he has chosen one status further complicates this narrative. Is Kirk only out for himself or is he actually of true empathy for other people? Of course another element often forgotten is that he's an orphan from an upbringing that appears to have been abusive. All these questions circle the themes of Ego, Moraltiy etc.
Spock is at the other end of empathy spectrum. He's fully capable of understanding right and wrong(unlike kirk), and yet is crippled by his inability to have his actions reflect his beliefs. Seemingly uncarring, willing to commit defacto suicide for his beliefs.
Added to this are many traits that make him the true hero of the films. He gets the girl, not because he's the cool guy, but because his intelligence and ethics impress uhura. This also puts a feminist twist that a woman is capable of making her own dating choices, by rejecting kirk. He's the true everyman of the first film, having his homeworld destroyed, being the core character of the plot, etc. I could go on and on about this actually.
Khan is a more extreme version of Kirk. He's clearly a psychopath, without remorse incapable of seeing people as anything less more than subhuman. Yet his apparent fixation on his 72 sugguest a more complex form of ehtics. Does he truly care about his people or are they objects needed for his plans of galactic domination.
While I might not be the best at explaining these premise be certain these are some fundamental questions that are not getting enough attention.
The classical good and evil motif has been exhausted.
In response Generation X was obsessed with the notion of the anti hero, everything is a shade of gray, and people are products of their environment and conditioning.
In 2010's we're in a time where both motifs are dated. Neuroscience is clearly showing us that some people are born bad to the bone(Psychopaths), and some are born truly good(People on the autistism spectrum have a very strong instinct for right and wrong, while pardoxically shown to have immense difficulties in translating these beliefs into actions).
What does this new found neuroscience mean no one knows, however I do believe these films will be proven to be ahead of their time with this aspect.