Biggest difference we saw when we dove PDC about a year ago was how you get to the boat. Don't expect to be waiting on a dock, and then stepping into the boat. PDC boat entry is via the surf, often carrying your gear with you.
We prefer Puerto Aventuras over PDC, for a couple of reasons. First, you board the boat from a dock; and second, we prefer the laid-back atmosphere in PA versus the hustle and bustle of PDC. The reef quality between the two (PA versus PDC) is comparible, but I will agree, you won't find the structure of Cozumel at either one.
Cenote access on the Yucatan mainland has to be a plus, however, so I don't think you can go wrong if you base in PDC.