Don't know if he'll be able to take such a beating again but if he fights smart then he definitely can go 12 and be competitive. If he leaves his self open then the chances of him getting stopped in a rematch are definitely higher.
Paulie won 4 or 5 rounds of that fight. Could he go 12 today? I would say no but he would definately have a chance. It just depends on how he fights and how much better Cotto actually is. Unlike Gomez, Paulie actually has the speed to give him a bit of trouble.
Paulie didn't "win" any rounds in that fight, Cotto "lost" them by only fighting in spurts and having a comfortable lead. When Cotto wanted to, he hit Paulie at will and beat the **** out of him. Watch the fight again, the fight wasn't close. It was only as close as Miguel let it be.