After watching the fight between Mayweather and Cotto this past weekend I did notice one thing that could cause Mayweather some issues if he were to ever choose to fight Pacquiao. Cotto pushed on him and May chose to roll the punches with his shoulder in the corner but many times he was vulnerable to a left hook (if you could find his head, great head movement). With the fact that Manny is a south paw and an obvious aggressive puncher I do believe he'll catch Floyd with some big shots that he's not used to catching.
With all that being said, I do know and acknowledge Floyd's ring intelligence and would tend to believe that he would keep the fight in the middle of the ring all night long to maximize his speed and counter punching ability. For that I believe he would win a decision and/or even KO Manny. If for some reason he chose to keep doing what he's done in his last several fights and let his opponent cut the ring off and pin him in the corner I think Manny would KO Floyd.
In general I just found it more interesting to think about since Cotto was able to get to him more than anyone else in recent memory and it all took place in the corner and due to Floyd for whatever reason, allowing it to happen (reminded me a lot of Roy Jones when his age went up and he basically would just rest on the ropes and it eventually led to his demise albeit Floyd's D is much better than Roy's ever was).