It is my opinion that Star Trek truly hit its stride with this episode. There's a certain effortlessness about the crew's relationship. The familiarity is infectious, and the audience can't help but sense it. It is with this confidence that the episode is able to achieve an even greater balance of plot and theme integration.
The crew encounters a group of genetically enhanced men from Earth's past lead by a tyrant called Khan. The episode's central drama centers around the connection between him and the Enterprise's Historian McGivers. Her obsession with the past is exploited by Khan to take over the ship. The only perceivable failing of this episode is that there is no discernible arc for her character. While in a moment of conscience she helps save Captain Kirk, she still ultimately chooses exile with Khan at the episode's end.
In fact, no part of this episode displays any form of arc, be it character or thematically based. While the content of the theme and conflict displayed may be interesting (it IS interesting: unhealthy ambition for human advancement vs. the natural ambitions of the Enterprise Crew) there is no inherent revelation or shift of development that results in a thematic conclusion. It is simply an acknowledgment of these two party's incompatibility that resolves what's presented as the dramatic conclusion. I can't help but feel that if the resolution came through significant developments of character or theme, the payoff would have been more effective.
Nevertheless, the conflict depicted is iconic and poignant. I take no issue with this. Seeing the Enterprise pitted against such an unhealthy ambition really helps define their mission for the audience. It is always when such extreme opposition is depicted that true colors can be revealed. This episode showcases the prime essence of Trek, even if it is wrapped in an slightly underdeveloped narrative.