Fist, lemme say that I love Isla Mujeres, and have spent a lot of time there, so I don't mean to sound like I'm down on the place. That being said, other than the whale shark thing, there's no real upside to going to a lot of trouble and expense to go over, or to make it a main vacation destination (unless you really want the small, quiet, relaxed vibe the island has, in which case it may be ideal).
The island is surprisingly small, and downtown itself is very limited, and is largely filled with exactly the same tourist-y shops you'll find everywhere else, and you'll pretty much take in the whole place, in a very short time. For the most part, diving Isla is gonna be going to the same sites they'll take you to from Cancun (which aren't anything special, either).
But, I wouldn't recommend Cancun over Isla, because Cancun is an absolute zoo, so I would enthusiastically recommend another trip to Cozumel (or even Playa) over Isla Mujeres. You have so many more options, basically at your fingertips (more room to wander and explore, more shops and restaurants, closer to many of the ruins, better beaches, better ocean diving, closer to the popular cenotes, etc.)
JMHO,YMMV, worth what you paid for it !
(working hard on Isla back in the day ! )
