We've been to Cozumel twice. The first trip was to SCC; the second trip was a Dive Paradise package at the Hotel Barracuda. Here's my comparison:
Both boats were relatively slow, but Dive Paradise had to stop at more resorts to pick people up. SCC simply loaded up and left. Dive Paradise does, however, offer a smaller, faster boat option.
The all-inclusive option at SCC was a GREAT convieneince for breakfast and lunch. Although we enjoyed our dinners at SCC, we had more fun exploring and eating in town.
On the other hand, it wasn't convenient to get breakfast prior to diving while staying at the Hotel Barracuda. Dining out in Mexico is a much slower paced experience than it is in the U.S. SSC got you a very quick meal in the morning and got you on the boats.
Divemasters with both operations were GREAT. SSC may have been slightly more personalized, as they attempted to have you dive with the same DM all week.
Hotel Baracuda had a TV; SSC did not. We didn't miss the TV, but we do like to check out CNN while on vacation.
SSC had a refridgerator; H.B. did not. This I really missed. At SSC, we enjoyed putting our bottled water in the fridge. The fridge came in handy considering SSC charged quite a bit for alcohol.
In a nutshell, I really liked SSC but would rather eat dinner in town.