If they fought now, I would lean towards Cotto. However, I think Berto should fight once more against a pretty good otrhodox fighter before fighting Cotto.
He's not ready for Cotto, at least not yet, he has to tighten up that defence. If Cotto is able to get to his body like Collazo, no way he sees the final bell. Also I'm interested to see if the Margo fight took anything out of Miguel. This is a fight that should happen down the road.
Bad comparison of Cotto-Corley fight because eventhough Cotto got hurt, he still won! The best punch in boxing is the jab. You can outbox your opponent with it, you can set up a combination after it. Cotto has one of the best jabs in boxing to offset and get Berto off his rhythm. It would be competitive, but we still have to see how Miguel performs against Jennings. Supposing it's Miguel before Margarito fight, Cotto would win by tko over Berto.
I see Cotto winning but i think he would have to get off of the canvas in order to do it. Berto is very strong and Cotto hasn't fought anyone with such blinding hand speed. At the end of the day, i think Cotto's better boxing ability, experience and body punching would be too much for Berto unless he could land some kind of crazy punch. Cotto by mid stoppage.
Cotto would destroy Berto. Berto has potential but has won the world title without fighting anyone. His first decent opponent and he struggled. That said we haven't seen how Cotto will respond to Margarito's demolition job.