I honestly wish he had just been "John Harrison" the terrorist with genetic augmentation. You could call back to Khan as a shadow. Not saying "Khan" not turning him into Khan. Not even going down that path. The "You can't do Batman without the Joker" is interesting, but ultimately the comparison doesn't work. Star Trek is way bigger than one all out villain. I think it would have benefitted from that, too. It would be new territory, relevant to the time, and not suffer from comparisons.