If you ask 20 veteran Cozumel divers which is the "best" Dive Op, I'm betting that you'll get at least 15 different answers. And the Dive Op that is best for you might well be on someone else's "I won't dive with them" list. You simply can't answer the question without knowing what you want from a Dive Op. Fast small boats or big boats with losts of socializing? DMs that will babysit a newbie diver or that will let you do your own dive? Big steel tanks for loads of bottom time, or is a 50 minute dive on an AL 80 just fine with you? Surface Interval on the beach? At a Beach Club? With Lunch on the boat? Valet service, or do you insist on setting up your own gear? There are a host of options on Cozumel, something for every taste. Like Drrich2, I really like Steel 120 tanks, Long SI at beach club, valet service, DMs who are great at finding the little interesting things that I wouldn't find on my own, smaller faster boats, and a Dive Op big enough to split up divers into groups with similar skills and experience. So, if it's my choice, I'll go with Aldora. But I've also been on a lot of group dive trips where we used Dive with Martin, a more budget option, less valet service, Aluminum tanks (you can get an AL 100 if you reserve it), SI on the beach, but not at a club and not as long. But great DMs - I really like Miguel and Roberto, and I won't hesitate to dive with Dive with Martin. So figure out just what you want from a Dive Op and then ask which one best fits your taste. As to locations, pretty much all the Dive Ops will go to all the locations in the Marine Park (though they won't all take you to the far south advanced locations, Maracaibo and Punta Sur); fewer Dive Ops will take you to the advanced dive sites at the north end; and, AFAIK, only Aldora will take you to the East Side (when the weather is right) or to the more remote sites that it has recently discovered.
---------- Post added April 5th, 2014 at 07:36 PM ----------
BTW, if you are looking for Lodging recommendations, I'm with gopbroek on the no AI - I don't have any firm opposition to AI resorts generally, but Cozumel is just not the place for it. Too many great restaurants, the people are incredibly open and friendly, and it's incredibly safe. Your choices for hotels kind of depend on preferences - I like staying in or near downtown, where I can walk to most of the restaurants at night, wander around the Plaza at night, and browse in the downtown stores without worrying about taxi money. Casa Mexicana is a nice hotel, very well located downtown, and if you choose to go with Aldora, it's a very short walk to its Dive Shop and its downtown pier. It has a nice breakfast buffet, but its "pool" is really only a small kiddie pool. Hotel Cozumel and Resort is south of Downtown and is a very nice Hotel, nice rooms, huge pool, but DO NOT DO THE ALL-INCLUSIVE PLAN. The food is, in my opinion, TERRIBLE. it offers a European Plan, room only, which is the way to go, IMO. It's not a bad walk into downtown to eat out at night. Farther south, there's Casa Del Mar, which I like; nice rooms, provided you go for the Superior rooms (the standards rooms are smaller and face the parking lot out back; not for me, thanks), decent pool (though the hot tub hasn't been working any time in my last 5 stays there), and a decent breakfast (though I often walk across the street to Ernesto's for breakfast). It's closer to the Dive Sites, and Dive with Martin will pick you up at its pier, but you'll spend more on taxis to eat out. Lots of other choices, including the big self-contained resorts farther south, and several places up north of Downtown, but the north end is a long way from the dive sites, and I've never stayed up there.