On my up-and-coming trip to Isla Mujeres (from Cozumel) I was thinking of taking the ADO from Playa to the Cancun bus terminal and then a taxi to the ferry but you just suggested a shuttle from Playa to the ferry. Is the ADO/taxi a bad idea? Is there a particular shuttle company you recommend?
If you set up a whale shark tour out of Cozumel, your transportation from Playa to the boat should be covered - this is the shuttle I am referring to - it's part of the package and is a specific/private van just for those going on the tour.
The boats leave Cancun which is only 15 minutes from Isla Mujeres - they simply pass Isla Mujeres on the way out - but then stop at Isla Mujeres north beach on the way back from whale shark tour and serve lunch - fresh ceviche and sandwiches.
If you're actually going to stay on Isla Mujeres for a few days, then ADO to Cancun Centro and then taxi the ferry terminal to Isla Mujeres would be the way I would suggest.