Pacquiao just outboxed Cotto and grinded him down methodically; Cotto did well in the first 3-4 rounds though but Pacquiao quick outburst and speed out speed in from all the angles were way too much for Cotto. Actually, Cotto won 2 rounds at most, which says a lot. Roach did an incredible job to work Pacman uppercuts and left hands which they knew Cotto would be vulnerable to. On the other hand, just as I thought, Santiago didn't do enough for Cotto and was mostly panicking in the corner rather than trying to quiet down Cotto and to get him back to the proper focus and to let him to carry the proper strategy.
Thus said, I will disagree that Cotto was still hurt from Margarito's defeat mentally; He was confident and was willing to last the full 12 rounds but he got very frustrated by Manny's speed and biggest number of punches landed and his focus went by the window a bit and Santiago was helpless for the task.