We dove with Pro-Dive when we stayed at the Sunscape hotel. They now also have an op setup at the Catalonia, and a couple of other hotels. We hated the Sunscape hotel (PM me if you're staying there and want details), but were happy with Pro-Dive. Their prices are a little high (we didn't know the difference then), but they are a good, conscientious dive op. Detailed briefing before each dive, including drawing the profile on a board. The boats are small, and we had a max of 10 divers on the boat; with a max group size of 6. We did the first half of our certification with them, and they definitely didn't "let us slide" on any of the skills. We had time for one "fun" dive, and the DM took his time poking around the reef, with no rush to get back to the boat. Nahuel (the head instructor at the time) checked everyone's gear on the boat, including a group that was working on their AOW cert. Tina (another instructor) is very patient, fun to dive with, and looks incredible in a white bikini.:drejnd: Tanks are put on the boat for you, but you have to walk about 1/4 mile to the marina schleping your gear, including the weights. We rented gear, so I don't know if they will store your gear overnight. They will store your bags and stuff while you go diving.
If you dive with Aquanauts, PA is a three minute taxi ride from the Sunscape or Catalonia. They have a good reputation, from what I've read. There were always a few taxis right out front at the Sunscape. PA is a 10-15 minute stroll from the Sunscape, but you'd better have a rolling case if you plan to walk with your dive gear.
Depending on when you go, they all do whale shark trips. It's a snorkeling trip, but everyone says it's a fantastic experience.
Pro-Dive picks people up from the hotels in the PA area. You may want to check to see if Aquanauts does the same.