For breakfast, The French Bistro has wonderful omelettes and crepes. Elements of the Island and Color de Verano also have specialty items. Great lunch spots include Picus for great Shrimp ceviche and whole fish right off the boat, Qubano for salads and Cuban specialties. Dinner is great at Olivia Tastes of the Mediterranean (link below for menu) The French Bistro (amazing lime caper fish filet!) Casa O's for romance, Almar Loung for Asian tapas, and Rolandis and Angelos in town for pizza.
The local Taquerias (Medina, Kash Kikan Chuc , many unnamed ones) ate wonderful too for pulled pork tacos and torta (carnitas) BBQ chicken and grlled ribs.
It is far tougher to find a bad meal than a good to great meal on Isla - There are no chains, plenty of small places with home cooking and general pride in their restaurants by all the hands-on owners. I think I ate consistently better on Isla than just about any other place I've visited.
For breakfast - First choice Cazuela M&J for one of their Cazuela's - think Mexican fritata. Close runners up - the restaurants outside of the public market and Color de Verano. Not that hungry - banana bread and coffee from Aluxes Bakery.
For lunch - my absolute favorite restaurant on Isla - La Lomita. Had two best-evers there - Chile Relleno and Chicken Mole. Playa Lancheros can be a bit tour-boatsy, but they are justifiably famous for their tix'n xic. Great guacamole too.
For Dinner - less fancy than some of the choices above - Fredy's. Basic Mexican. Also the source of my all-time favorite restaurateur quote. A customer wondered why the chicken was taking so long. "Senora, we haven't even killed it yet." Excellent pork chops.
Some Isla Resources -
Two chats (one for new-comers, one for residents): http://www.islamujeres.info/ Go to the "Sharing Isla Section."
The most useful $8.00 you'll ever spend: Map Chick's map of Isla Mujeres - http://www.cancunmap.com/isla_mujeres.html I just checked and they are closing out the current map - a new one will soon be published. Since you're leaving soon, go for last year's version. It is an invaluable tool.
I spent two weeks last year eating Isla - http://www.hollyeats.com/IslaMujeres.htm
I'm going back for three weeks starting tthe end of January, so please share your finds.
First meal off the ferry - one of the seafood restaurants that line the Caribbean beach where the ferry lands for cerviche or a shrimp cocktail. Picus and Minino's are good bets.