I've heard from Cozumel locals that the big protection rackets that are run on many retail Riviera Maya businesses have not come to Coz and there's a strong police (local and Federal) effort to prevent that.

I do get your point about cruise ships and to me it's just a matter of staying away from the big "plaza" area when the ships are most prevalent. While I do like the entire island, staying at the big hotel areas south of town aren't for me as they mainly cater to families who go for the all inclusive experience and the mega resort kind of trip.

We've never stayed in Cancun and our only onshore RM stay was one trip to Akumal which was OK but not great. I think you're better off on the two islands, though I do agree that the entire area is getting pretty crowded overall and crime is a concern here and there.