We have been to Isla Mujeres and Cozumel each one time within the last 5 years and I would say the answer to your question depends on your vacation objectives and expectations.
Which has better diving (i.e. dive sites)? Cozumel, hands down no contest. BUT Isla Mujeres is not bad at all and whether you will be disappointed and wish you were back in Cozumel depends entirely on what else you want from your vacation. If you want more out of the surface interval and a friendlier, more laid-back atmosphere, the Isla Mujeres is definitely worth a try. Outside the very center of the tourist district, the restaurants are twice as good as those on Cozumel at about half the price. Do rent a golf cart (forget the car) and drive all over the place but get a hotel in the north end so you can walk to the grocery store, beach and dive shops. Very importantly, unlike Cozumel, the island is not a slave to the relentless rhythm of cruise ship arrivals and departure.
Re. the diving, I have to agree with Jungle Diver above. The reefs are beautiful, shallow and sunny. You could leave the strobes at home but do bring the wide angle. They are full of life in the extreme. There are many dives where the colorful reef fish are so dense that you *literally* can’t see the reef. The MUSEA is not great but it is fun and interesting to take in once. I don’t know if would really call it a tourist trap. Garrafon Park is a tourist trap. Stay away. Also, on Isla Mujeres you can actively participate in egg harvest as sea turtles lay their eggs and attend a hatchling release both for free.
For whalesharks, I would strongly recommend Capt Tony Garcia. For an immaculately cleaned and maintained hotel with a proactive, warm, attentive staff right on the beautiful north beach, I would strongly recommend Hotel Ixchel (hotel rooms and apartments with kitchens).
Which has better diving (i.e. dive sites)? Cozumel, hands down no contest. BUT Isla Mujeres is not bad at all and whether you will be disappointed and wish you were back in Cozumel depends entirely on what else you want from your vacation. If you want more out of the surface interval and a friendlier, more laid-back atmosphere, the Isla Mujeres is definitely worth a try. Outside the very center of the tourist district, the restaurants are twice as good as those on Cozumel at about half the price. Do rent a golf cart (forget the car) and drive all over the place but get a hotel in the north end so you can walk to the grocery store, beach and dive shops. Very importantly, unlike Cozumel, the island is not a slave to the relentless rhythm of cruise ship arrivals and departure.
Re. the diving, I have to agree with Jungle Diver above. The reefs are beautiful, shallow and sunny. You could leave the strobes at home but do bring the wide angle. They are full of life in the extreme. There are many dives where the colorful reef fish are so dense that you *literally* can’t see the reef. The MUSEA is not great but it is fun and interesting to take in once. I don’t know if would really call it a tourist trap. Garrafon Park is a tourist trap. Stay away. Also, on Isla Mujeres you can actively participate in egg harvest as sea turtles lay their eggs and attend a hatchling release both for free.
For whalesharks, I would strongly recommend Capt Tony Garcia. For an immaculately cleaned and maintained hotel with a proactive, warm, attentive staff right on the beautiful north beach, I would strongly recommend Hotel Ixchel (hotel rooms and apartments with kitchens).