Thanks for the input everyone. It looks like my choices may be also limited by the packages offered through Expedia for the Charter flight we're planning on taking.
Here is what has been suggested for hotels so far:
Wyndham (Reef Club) - available
Fiesta Americana - available
El Cid - available
Scuba Club Cozumel - not on the Expedia
Cozumel Palace - appears to be booked for time we are there
El Cozumeleno - available
For dive shops:
Blue XT~Sea
Deep Blue
Just to help you narrow your hotel choices, I'll give you some extra input:
Wyndam - I personally wouldn't recommend this hotel. It is far enough south of town to limit your dive site options...basically any sites north of your hotel are out unless you are willing to taxi back after a dive. Most dive ops won't pick you up for a night dive there either, so you will have to taxi to the marina for a night dive. There will also be a $3 per day/diver fee charged by the hotel to access the pier...and dive shops are not going to pay this fee.
Fiesta Americana - Much closer to town ($6 cab ride vs. $15); AI optional, and it's location will not limit your dive site options. Any dive op can pick you up at the pier. Good choice.
El Cid - Another good choice. Close enough to town to walk if you are a walker, no limitations on dive sites, newly renovated. Any dive ops can pick you up at the pier.
Scuba Club - This is truly an all-inclusive. You would have to dive with their onsite operation because their package includes the diving, meals, and lodging.
Cozumel Palace - The nicest of all of the hotels and in fact, aside from the Presidente...the nicest hotel on the island. Great location, All-inclusive (not something I recommend because Cozumel has so many great and inexpensive diving options), no dive site limitations, and any dive op can pick you up at the pier. Good choice except for the obligatory AI (meaning you have to pay for it whether you use it or not).
Cozemeleno - Not recommended for divers because of it's northern location. Dive ops do not provide pick-up service at the northern hotels, so you would have to taxi to town or wherever your boat departs from each morning to catch the boat. Otherwise, it is a nice hotel, but again is obligatory AI and I've heard the food is horrible...as are MOST AI's.
I hope this helps!