I'll continue everyone's positive assessment of the Palace. I stayed there a couple times and would have gone back except that I started traveling on my own and they don't offer a single rate. Besides that complaint, which only pertains to single travelers, my only other nit picking is that it can be loud until around 10 pm if you plan on heading to bed early because of the outside entertainment. They're good at cutting off the noise at 10, though, unlike other places where sounds can carry on late into the night (there was a band at the corner bar one night during my last stay at the Bahia Suites, for example, which played loudly until around midnight). The other noise complaint commonly mentioned on Trip Advisor and which I can concur with is that the marble floors in the corridors, while beautiful, magnify the sounds of footsteps and the acoustics of drunken voices. Some recommend stuffing a towel to close the gap at the bottom of the door to mitigate that issue.
But neither of those nits detract much from the otherwise excellent overall experience. Service is impeccable, the food maybe not up to the quality of the best island restaurants, but certainly as good or better than many, drinks high quality, and the rooms are spacious and comfortable. My favorite part of the palace is the little surprises you find there. Every night they set up a table in the lobby which might have some interesting and tasty appetizers one night, a guy making flaming Mayan coffees the next. One afternoon we were in the pool and a parade of waiters came around carrying freshly made chocolate dipped ice-cream bars of various flavors. The restaurant menus are very varied, enough so you won't get bored eating there for even a few weeks, and the lunch buffet is amazing - that's coming from someone who generally detests buffets except at breakfast. I can't even comment on the breakfast buffet, though, because I always utilized the room service - can't beat the convenience of having your food delivered while you're prepping your camera and readying yourself for the day's diving.
All that said, I'll focus on your question of whether Aqua Safari is a good choice. It probably is a "good" choice, but I'm pretty sure you can do better. The nice thing about Cozumel is that there are a range of dive shops that will pick you up right at the dock as well as store all your gear for you so you don't even have the hassle of carrying stuff between the Aqua Safari shop lockers and the boat. My favorite dive op, Living Underwater, uses steel 120s for extended profiles, has a huge camera tank on board, and even stores your wetsuit so you don't have to drag it with you over those slippery marble floors, plus owner/DM Jeremy is one of the best dive guides I've ever had the pleasure to follow. There are other excellent choices of dive ops as well. I'll put in a plug for Blue X-T-Sea if you don't want/need the heavy steel tanks - she has new fast engines on her boat and a DM with over 10,000 dives on the local reefs. Either way, you can't go wrong.
You probably won't go "wrong" with Aqua Safari either, especially on a first trip there and at your level of experience. The only complaint I've heard about them is that it may be tough to schedule all the "free" dives you want at busier times depending on how many boats they're running. But if you want to pay real money to dive, you can get really pampered with either of the two boutique shops I mentioned plus a host of others offering similar amenties and some of the best dive guides in the business anywhere. The problem with using an outside dive op is spending all those credits they give you. There are a number of excursions they offer, but which may conflict with your dive schedule. I would send J off to the spa for massages up to the maximum permitted for that use ($300) and we'd "spend" the rest on the "romantic dinner for two" and on bottles of wine from the very pricey wine list. It almost seemed a waste of the credits to use them on frivolities which we might have otherwise bothered with - since the "free" wines on offer are adequate and so are the restaurants - but I come to Cozumel to dive and therefore my first priority is diving with the best dive op even if it takes more out of my pocket. YMMV.