We have stayed at Hotel Cozumel several times. It is clean and an easy walk to the water.
We would prefer not to dive with them. Try Aldora or Jeremy at Living Underwater. Both run six pack boats and Jeremy has a bit more personal service and a smaller operation. Both do long dives with up to 120 cubic foot tanks. We always bring hard candy and Jeremy does like Werthers.
We prefer to stay in town at one of the even less expensive places. Casa Mexicana is downtown. It is a short walk to the pier for Aldora and Jeremy uses their pier as well. Jeremy will pick up your gear at the hotel and have it assembled and ready to go on the boat. Aldora has you drop your gear at the office and it is ready on the boat. We have done a night dive with Aldora on the first day. We got in around 1 and dropped the gear off and they picked us up at 430 or 5 for an afternoon and then night dive extravaganza.
At Casa Mexicana there is a buffet breakfast included with the room. We don't drink so a full meal plan with alcohol isn't really a bargain. I may have one or two drinks during the week and my wife has one after diving is done for the week. They also have several other properties that are around downtown. Farther away from the water usually means less expensive.
Do tell them you want a room facing the ocean but sitting in the lobby is good for us. The wifi works good there too. We figure we don't spend much time in the room so why pay for the view. Clean is good the rest works itself out.
As for the meal plan. There a some really nice and relatively inexpensive restaurants in town. Wherever we stay we eat a light breakfast and lunch and go to a different restaurant each evening. Ask the guys on the boat. They won't steer you wrong.
Hotel Cozumel. A little quieter and a couple of dollars for a cab ride to town and back. It is walkable but it takes 20 minutes or so.
Mexicana A little noisier but we are already in town.