He could not deal with Manny's speed, Khan is faster and has a better reach than Manny. I think also at 147 Khan's power will be respected, Cotto won't walk though him.
Manny is an ATG for crying out loud and way way better than Khan. Cotto beat faster guys than himself before, but Pacquiao had so much more than those guys. He used unpredictable angles with his shots (how often do you see a southpaw drop a guy with a right hook to the body, leaping left hand combo?), toughness in absorbing head and body shots, footwork, etc....It's like comparing Chavez's dominating performance with the fast Camacho and using that to gauge how he would do against the fast Whitaker. People are expecting too much out of Khan. He is just a guy who is largely getting by on his physical gifts of speed and range/frame. Little imagination, too robotic and not fluid enough, one dimensional, poor footwork, leaky defense. There have been a ton of fast guys who have boxed and you need much more than just speed to be great. His flaws can make him fun to watch because of his vulnerability (the Maidana fight for instance), but people will be greatly disappointed if they expect Khan to be some sort of P4P leader.
Cotto brutally stops him if he lands the right shot. Khan would not handle the punches that mosley or margarito took from Cotto.