I've been diving with Aldora for several years and have always found it to be a good value. A two-tank dive with Aldora does cost more than other Cozumel dive ops, but I think you get what you pay for. They use high-pressure steel tanks, usually 100s and 120s (I think they also have some 80s), which allow for long dives, averaging over 70 minutes, even on deeper sites where your max depth will be around 100 feet. The staff is great, the boats are nice, and you get great service. In two dives, we usually log enough time to equal three dives with most operators. On a dollars per minute underwater basis, I think it's a good deal.
Their boats pick up from the Villa Aldora, north of town, at the Aldora Pier, downtown, and at virtually all hotels/resorts south of town. Most dive ops will pick up from resorts south of the caleta and some pick up at the Aldora Pier.
Aldora's dives are definitely not restricted to the 40-60 ft range. Second dives might be in that range, but first dives are deeper, generally 80-100, sometimes a little deeper. There must have been some confusion in your conversation with them. If you were talking to Kay, who handles bookings at the Villa, she has been around for a long time and knows the operation.
I've seen plenty of stuff on the shallower dives. It might have been a lot of sand and rubble right after Wilma, but that's over ten years ago. There is a lot of good diving on shallower reefs.
If the Villa doesn't have a room to suit you, which can happen because it's a small property, I can't help much with lodgings.
