Its a pretty tough comparison since they are so different. I loved the cenotes and jungle. Cabo has nothing like that. As has been mentioned the beaches in Cabo are not all swimmable and not the best.

Fishing in Cabo is a must and I think the food is also better (Tacos Gus ftw). Snorkeling is just as good if not better in Cabo. Try and find someone that will take you on 4 wheelers to La Candelaria, its a really cool day activity. Oh and in Cabo get a place close to the actual marina if you dont rent a car. You will be stuck at the resort or end up spending your life savings on taxis otherwise.