The primary diff between dive trips on Cozumel is whether the boat you go out on is large or small. On the large boats, they tend to have the site scheduled in advance rather than polling the divers, which makes sense, since consensus is more difficult to achieve with more opinions in the mix. Also, they tend to be more restrictive on bottom times, for pretty much the same reason; they have a lot of divers with varying degrees of experience to handle, so to protect themselves and their divers they tend to play to the lowest common denominator. They tend to play it safe; no surprise there.
On a small boat, the tendency is to poll the divers for a destination and to let the divers' air consumption and computers determine the length of the dive. Fewer divers = more flexibility. Of course, these traits are not universal.
Some ops on Cozumel offer both large and small boats.
Within the small boat trips, there is a secondary division. That's between the "no frills" operations who dive on AL80's, provide water and a basic SIT between dives, no mas. The more premium operations charge more and offer a variety of amenities such as access to larger tanks, keeping and cleaning your gear between dive days, snacks or lunch provided between dives, SIT's at beach clubs where a docking fee is charged, etc. It is for the diver to decide if these extra features are worth the extra expense.
There is a lot of competion for business between dive ops (although it is very amiable); as a result, most if not all of the dive ops on Cozumel are very good, within the scope of what they offer. Most of the complaints I have read about particular dive ops stem from divers picking the wrong op for the experience they were wanting to have, and not from the dive op being "bad".
My US$0.02, anyway.