The dive sites around Cancun are very mediocre compared to Cozumel, the reef systems and topography are totally different between the two. If you want the best of what's offered in the region of Cancun, Isla Mujeres and Cozumel, it's hands down without a doubt going to be over in Cozumel. I've dived all three places and there is no comparison, the diving in Cancun and Isla Mujeres will put you to sleep compared to Cozumel. The biggest dive attractions around Cancun and Isla Mujeres are the under water sculpture garden near Isla, a few wrecks and sleeping shark cave dive site east of Isla. Keep in mind sleeping shark cave is the biggest over hyped dive in the region. There are no sleeping sharks. You might stumble across a nurse shark under a ledge, but you can do that anywhere between the three areas we are talking about and the reef at that dive site is nothing any different then any of the others around Cancun or Isla. If all you want is some fun, average caribbean diving, it's near Cancun and Isla, you can have some nice little relaxing dives there, but if you want as you said the best of the region, it's across the channel at Cozumel because the diving there is consistently better, all drift diving, giant coral formations, walls, swim thrus, huge variety of fish life.... Isla, Cancun, Play Del Carmen, Akumal, Tulum are about vacationing, Cozumel is about diving.
There are a few dive sites outside of Cozumel that are very good for specific reasons, however they tend to be seasonal, and they are individual isolated sites. The bull shark dive at Playa Del Carmen, to see bull sharks. The gun boat dive near cancun to see squadrons of eagle rays (seasonal). Tortugas dive site near Playa Del Carmen to see a ton of sea turtles however isn't seasonal I believe. The one caveat about diving around Isla Mujeres is if you're diving the northern and eastern sites you're basically in open ocean and you have the chance of seeing mantas, dolphins, whale sharks, sharks etc... however it's only a chance, the opportunity is there, but the chances aren't something you could count on. You might dive the same dive site 10 times and never see anything but jacks and snapper, but that 11th dive you might run into a dolphin.
I'd also recommend second thinking seeing the whale sharks at Holbox. You're most likely going to be in low viz green waters. The operators from Isla Mujeres are going to take you out into blue water to see them with better viz. Some do pick ups at the port of Morajeles which is at the end of Cancun saving you a ferry ride over to Isla Mujeres.