If your son didn't like the little fish then I would not recommend Cemetery Reef for swimming either - lots of them that 'swarm' and its a little overwhelming at first. Have you heard about the Pirate Ship? It might be something they would enjoy... they dress as Pirates and were very entertaining the time I was on it. It also seemed very family oriented (unlike what I have heard about the Mexico boat cruises). Here is the link for that if you would like. http://www.jollyrogercayman.com/
From reading other posts it seems that renting a car may pose problems as far as time goes - you have to grab a shuttle to the airport, then drop it back off at the airport and get back to the ship - depending on how much time you have in Cayman, it might be rather hectic. I was in GC for an extended period so had not considered the time constraints before. If you wanted to see the Turtle Farm, Hell and go on the Pirate ship (or even hit a beach) you could likely do it more efficiently (timewise) by taking a cab.