A few years ago before the property to the north was built up (Aura, Sabor) my wife and I were walking on the beach past the property, found no one staying there at the time and asked a maintenance guy for a tour and he obliged us. It looked very nice inside and had all the amenities. We especially liked the rooftop patios. Since then we have noticed that at least from the outside, it appears well maintained. This place we thought would be great for group trips and the price was reasonable at the time. We stay near to the Villa Dos area and have been to Cozumel about 40 weeks over the years.
We also understood that the owner lives on the property and always seemed friendly.
San Francisco beach has become busier due to the hotel and condo construction, proximity to the San Francisco beach club and cruise ship passengers at the same beach club but Villa Dos is still a bit separated from both. The beach bar to the south should shut down in the evenings.
The snorkeling at San Francisco beach is not bad but I think not great. Its mostly sand and not much coral but there are some structures that contain more sea life. There are fish in the area jacks, trunkfish, needlefish, maybe flying fish, stingrays, in addition to maybe some small lobster and eels if there are structures. The good snorkeling is done via boat to the reefs. Its too far to swim especially with currents which are generally South to North but can change. We dive but if I were to snorkel I would do a twilight or night snorkel where you are, go to Chankanaab, or go to Colombia shallows or other site by boat (more $ tho for the latter).
Be careful not go too far off the beach as it has high boat traffic (and fast boats) many dive boats, large catamaran snorkel boats, sunset cruise boats and parasailing boats.
Take care with the jet skis drivers rented at San Francisco beach club during the day. Some of them lose their common sense as soon as they hit the water.
Having said this, San Francisco beach is a very nice beach and I think among the top beaches on the West side. Many people enjoy it.