I couldn't disagree more about Khan's character in TWOK and STID.I think it's a really, really dumb story on almost every level, but that's another discussion. My point here is that it wasn't a story about Khan. Not the Khan we met in "Space Seed," the brilliant leader and tactician with qualities that Kirk could admire despite his ambitions for conquest. TWOK threw away all that potential in favor of making him an obsessed madman, a radically different character. Sure, the film justified the change with all he'd been through over the years, but it was still a complete transformation of the character, with basically just the name remaining. It didn't really build on the potential of "Space Seed," just tossed it aside in favor of a stock "revenge against the hero" plot. STID's Khan is closer to the original "Space Seed" version of the character, with that self-discipline and cunning and ambiguity intact.
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Honestly, even if I were lazy enough to create original SF by filing the serial numbers off of a Trek story, "The Doomsday Machine" is not a story I'm motivated to emulate. I think it's massively overrated. It's TOS's equivalent of a shallow FX-driven action blockbuster, visually impressive for its day but very superficial and often ridiculously exaggerated. I think the main thing that makes it work is Sol Kaplan's magnificent musical score, which elevates the material beyond its merits. If the episode had been tracked with stock music, I don't think it'd be half as well-regarded.
Even if you don't like the madness/revenge Moby Dick angle of TWOK, Khan in his right mind would probably have attempted to defeat Kirk in a similar manner once he learnt Kirk was tangentially involved with the Genesis team. I don't think his wanting to 'defeat the plans of Kirk' was too much different to his character in Space Seed. Get a guy who's previously defeated him makes sense to me.
In contrast the Khan in STID was so bloodthirsty - an entirely different guy from the dictator on Earth in the 20th century who ruled with no massacres (unlike his fellow augments) and seemed content to rule over his "sheep" rather than kill them. If they restored one of the other augments instead of it being Khan then I could understand STID.
I thought Doomsday Machine was a great episode. Well written and acted.
However I don't want a movie based on it as we've already had the episode and what more could a movie add to the basic plot.
If you want another movie plot my idea is to do what TOS did originally - get some scifi writers to write a plot and pick the best.