Add me as another vote against All Inclusive on Cozumel, unless there is a VERY good reason for it (like you're traveling with kids, and you want them to be able to feed themselves without constantly giving them cash). Far too many good restaurants in every price range with a wide variety of cuisines on Cozumel to get locked into an AI. There are a few AIs close to town, but both with downsides. Cozumel Palace is an easy walk to town, and pretty decent food (from what I hear), but very expensive. Cozumel Hotel and Resort is a bit farther away, huge pool, comfy rooms, still not a bad walk to town, but, IMHO, the food is TERRIBLE. The good news is that Cozumel Hotel offers a breakfast only option, and while the breakfast is nothing to write home about, it's certainly edible, pretty good if you stick to the omelet station. The coffee is swill, though. Best downtown option, IMO, is Casa Mexicana, much better breakfast buffet, included in the room, and very convenient to all restaurants and a number of excellent dive ops. But Casa Mexicana has only a very small splash pool, IMO a real downside for a July or August trip when it can get very hot and muggy. For me, a big pool is a must for a July trip to Coz, and I'd probably opt for Hotel Cozumel at that time of year, just for the pool.
The Whale Shark trip is well worth it, but from Cozumel it is an exhausting all day trip, catching a very early Ferry to PDC, a van to a marina up north of Cancun, and a long boat ride out to the Whale Shark area. Plan on getting up very early, being gone all day, and returning to Cozumel about 5:30 or 6:00 completely wiped out. And prepare yourself for a real cardio workput snorkeling with the Whale Sharks - it's NOT like your lazy snorkel over the coral reefs, it's hard work. But amazing being in the water within a few feet of a fish the size of a school bus.
BTW, the house Dive Op at Hotel Cozumel is Dive Paradise, certainly a competent operator, and I won't say anything negative - I've been diving with them before, they were fine and I wouldn't hesitate to go with them again if I were on a group trip and they were the designated Dive Op - but they are not my cup of tea, and wouldn't be my first (or second, or third) choice on Cozumel if the selection was up to me - DSFDF. You are NOT stuck with the house Dive Op at any hotel - check out any of the highly reviewed Dive Ops on this board, Aldora (my preference, HP Steel 120 tanks, long bottom times, long SI at beach club, lots of boats, sorting divers by experience and ability, etc.), Blue XTSea, Liquid Blue, Tres Pelicanos, and others, all with their own rabid supporters and cheerleaders, any of which will almost certainly give you a great dive experience.