I'm not too hip on the AI thing either, you have a tendency to just stay to the resort and not get a real feel for what Cozumel is all about. Plus you can stay at a regular hotel and eat at the restaurants around the island for less money and more variety.
Most boat diving is extra at the AI's I do believe if you decide to go that direction. Shore diving is usually included at all resorts AI or not, but the real thing is out on the reef.
Hotel suggestions?... La Ceiba great location, photo shop on site good restaurant, good shore diving and snorkeling; Casa del Mar (cheap, clean, no frills, built for divers, accross the street from the beach by La Ceiba); Fiest Americana, further south than La Ceiba but some friends just stayed there and liked it.
Just make sure your south of town, it will make it easier to get on a dive boat as most of the diving is that direction.
someone suggested the Melia, it's way up north, kind of out of the way.
Dive ops?...Blue XT Sea, Christi is on this board quite a bit and is highly regarded,;Dive with Martin, good folks with good prices, high recommended by friends,;Blue Bubble I personally have dove with them many times and have always been very impressed with the DM's, small groups and fast boats.
Inexpensive restaurants?...Ernesto's fajita factory, Casa Denis, Playa Corona, La Mission... the list goes on and on.
hope this helps
God bless,
the shark