This is a "wolf in sheep's clothing" episode, like Wolf in the Fold. Unlike Wolf, however, Space Seed has a beautifully slow reveal. Starting with the uncertainty over what they've even found. First, a derelict ship. Next, there are some life signs, but not human. Next, oxygen atmosphere automatically comes on. Next, per McGivers, it's a "sleeper ship" -- suspended animation -- very cool. Then, the leader's sleep unit automatically starts reviving him, starts to fatally fail, but his life is saved by Kirk's and McCoy's expertise, whew! Then, it takes a long time to even identify who Khan is. (No automatic facial recognition software in the future apparently.) Montalban's slow burn is also wonderful, culminating in "I intend to take this ship!" Yikes!
Also very well done is the emphasis on history, through the character of McGivers. The usual cheap shortcut is just to list off a series of historical items and tack on a fictional one or two at the end. In this case the fictional extrapolation is given to us in the flesh! And of course the intrigue is even richer when the fictional near-future has to do with Earth events -- a World War 3, eugenics.
And this ties right in to the great tug-of-war, again through McGivers, which is the central conflict of the story. First her bona fides as a professional and loyal crewmember are established when Kirk tries to reprimand her. But then the magnetism of Khan, and his cunning exploitation of her weakness for strong men, turn the tide so completely that she promises to do whatever he wants. By the way, a good, if extreme, depiction of the psychological dynamics of domestic violence. In the end, McGivers cannot tolerate the violence against others, and in particular against Uhura. Her loyalty re-emerges and she double-crosses Khan to save Kirk, asking only that Khan not be killed.
Per formula, Khan and Kirk have to have one final one-on-one hand-to-hand before Khan is finally subdued.
But then Kirk once again shows mercy, dropping all charges and planning to maroon Khan and all his people on an uninhabited planet, for them to tame. He even gives McGivers the choice to join them to avoid a court martial. She chooses to stay with her abuser I guess, gahh.
I noticed on this close viewing how rushed and sloppy the pacing got in the second part, the action part of the episode. There is even some tape or something visible on the floor of the sound stage, ahem, I mean hearing room.