Cotto is more skilled and can outbox Margarito all night long. He will also hurt Margarito. Margarito is okay but no where near as good as he would like to think. With the exception of 2 other fighters Cotto is unbeatable at Light Welterweight.
Margo is a one-track minded boxer whereas Cotto showed versatility against a more aggressive than expected Mosley. Cotto can adapt, Margo not so sure. The difference in size won't impact the outcome nearly as much as the difference in speed and skills, both of which advantage Cotto.