I'd have to say Khan for both rounds. In round one, Wolverine wasn't all that impressive with just his bone claws. He wasn't martially adept really. Khan was martially adept, stronger, faster, more ferocious, and smarter. In round two, Khan was one gunslinging badass with those weapons. If it was just a random dude with those weapons, I'd give it to Wolverine. But Khan made gunslinging look like a dance. He'd nail Wolverine.
Khan takes this.