Of course, the second explanation is at first my in-universe rationalization: they had to be docile enough to follow Khan.
I'd argue that not putting a word edgewise with Khan is a clear sign of superior intelligence!
Wrath of Khan reimagine Khan as leader of a group of Arayn youths who would be completely lost without him.
Or, in other words, the plot of the movie put him in this new situation where he led a group of Aryan youths. In the fifteen-odd years, Khan's age-mates would have died out, either because Ceti Alpha Insert-Numeral was a really hostile place, or because the aging Khan really, really didn't like competition...
In Space Seed, his people were contemporaries, who followed him but you got the impression they could all be extremely dangerous.
...A great reason for Khan to get rid of them!
My biggest issue with Khan is in WoK, when he is defeated because he doesn't understand that space is three-dimensional. A child would understand it, let alone a super genius warlord. I guess they wanted a very basic battle tactic which anyone could understand, but it did Khan a huge disservice. He became Derp Khan.
I don't really see how "understanding" would have helped Khan any, or how three-dimensionality would have played any role in Kirk's victory. The two ships were circling each other in a soup thick enough that they could pass each other within a few hundred meters and not see a thing. Kirk could have sidestepped to port or starboard just as well as down, and the end result would have been the same.
The mystery here is, how could either side re-acquire the other in the crosshairs at all? This happens several times in the fight, even though the only means of locating the opponent seems to be visual scanning of the immediate vicinity, through so much noise to the signal that only point-blank targets could be spotted. Khan is shown scanning dead ahead, rather than down where Kirk lurks - but that's not an example of 2D vs. 3D thinking, that's simply 1D necessity in an environment whose dimensionality is irrelevant. Khan would have been no better off scanning down, or up, or to port, or to starboard: he needed to be vigilant in the whole 4pi sphere around the
Reliant, and he
could not. But neither could Kirk.
The battle seemed to be decided by two skippers guessing where the other one might be, and Khan guessed right just as often as Kirk did. Both guesses are unrealistic to the extreme, given the conditions, but neither makes Kirk the more skilled commander. The outcome just shows Kirk had better luck.
Timo Saloniemi