What's that old saying go like.....It takes a great small fighter to beat a good big fighter.
I feel where you coming from.
Khan got some nice attributes, but he's not more skilled than Canelo. Not even counting his chin, but that footwork that he can't seem to control makes problems for himself all the time. His feet will be moving away, but he's still punching and vice versa. Plus his overall defense is average as hell.
Shane prolly had more natural talent and attributes than Winky, but Winky definitely had more skills. His size and strength helped reinforced his gameplan, so it did play a part, but that jab and defense is what made shyt happen.
Ditto for Tito and Hopkins. Tito never beat someone bigger than himself that had more skills.
Usually if the bigger guy is more skilled, he pretty much dominates the smaller guy. It's like double the advantage
Roy beating Ruiz is a good example of a great fighter with more skills beating a good fighter (ok Ruiz, being good is a stretch, but he was a solid B level guy, decent heavy)
Duran beating Barkely is up there too.