The more I think about this fight, the more I think the key difference will be footwork. Look at Martinez's last two opponents, Chavez and Murray, there were both essentially plodders. Cotto has some of the best footwork in the game (just look how easily he closed distance on Rodriguez in the last fight, or heck, just watch that video from this week of him hitting the heavy bag).
Martinez is fairly mobile, but his footwork can be a bit clumsy (and hes usually moving against physically bigger plodders, making him look even more mobile). Using his excellent jab and footwork, I think Cotto will be able to get in and out when he wants, and that will be the difference.