What I find particularly sigfnificant about this scene is that intelligence alone proved insufficient, and this wasn’t compensated for by “heart” or emotion or anything crappy. Kirk was the more experienced commander (Khan shouldn’t have even been able to navigate the Reliant in the first place, but no matter) and this won the day. Compare that to interminable episodes involving Wesley Crusher, who can casually save the day when older, more experienced personnel are helpless, or even the first film when a human’s ability to “leap beyond logic” saves the day. Blech. You win battles by killing the other guy, not just outsmarting him or empathizing with him.
I agree with your entire post except for this. But let me explain why…
In Space Seed, Khan had access to the computer files and used these to learn about the ship’s (NCC-1701, no bloody A, B, C, or D) systems. He put this book knowledge to practical use in actually taking over the ship. In TWOK, he had Chekov and Paul Winfield available to him to fill in any gaps from the last 20 or so years and no doubt he` set to reading the ship’s manuels again. No, not on screen, I’ll grant that. But the canon precedent from the TOS ep works by implication here.
But as you’ll recall, he didn’t actually take the Enterprise anywhere. He tried various means of encouraging the crew (including killing Kirk) to join in with his gang because he needed their specialized training. And one assumes the Reliant is a far more advanced ship. The novelization of TWOK, I’ll admit, makes the matter clearer, with “the engine company” remaining aboard the Reliant, subjugated by Ceti eels. Most of the 300 crew was marooned on Ceti Alpha V, only ten were killed.
In general, the improbable ease with which unfamiliar technology is mastered is a common theme. Notable cases included the Kazon landing a hijacked Voyager flawlessly, something its own crew had done only once.
It’s not something I’d fret about in an otherwise amazing film, but I remain glad that intelligence alone got clobbered by intelligence plus experience.
Incidentally, this is just reminding me of how I wished the “augment” episodes of Enterprise had ended…