Mystique fighting against normal people has been shown to be superior to Khan fighting against normal people. Faster, more skilled, more agile and flexible, and stronger. She's sent people flying farther than he did in direct comparison.
I'm still not convinced. I mean she does beat up normal people in a more dynamic fashion than Khan but physically he's still more impressive from what I could tell.
Mystique is more skilled but she's not damaging Khan. His strength and ferocity will win out over her agility and fighting skill. During the assault on the Vengeance he kicks a man 15 feet up in the air.
He's also ridiculously more intelligent and tactically aware.
Her only hope is some kind of stealth assassination and he would have no prior knowledge of her changing ability. Otherwise he'd find a way to detect her mutant genes as Trask did and root her out before she could kill hing
Personally I think this is a very close match, one which Im glad is evening out in votes now. Im really not sure who would beat who in HTH really, I might side with Khan as I think him more cunning and overall intelligent, but this would be a close match, that could certainly go to either.
See, this is a character in Khans power level, providing an even match overall. Pitting him against Jedi Masters and Sith Lords, and expecting him to win, is just silly really.
Mystique was able to create a "copy" of Wolverine's claws which were sufficiently sharp enough to cut metal. She could use those (along with her superior skill and speed) to cut Khan to ribbons. Unless, for some reason, that doesn't count as h2h.