To be honest, I'd put that way down on my list of things to do with sequels. I am happy to shed "canon" precisely because it opens up NEW possibilities. I don't want to rehash old ones.
Exactly how I feel. Besides, the Khan everyone remembers is a revenge film. Space Seed v2.0 wouldn't be as intriguing on the big screen, nor would it make a good starting point unless they really went to Dark Knight levels of writing. Which wouldn't work.