I've done Batman/cave wishes (not the San Fran one, but two others - one was my kid and one I was helping out as a volunteer on the day of), and trust me. They exist.
One of those Batman wishes, the kid was among the happiest I've ever seen a kid about his wish. Just a total superhero that day. Most of my Disney wishes have been great, and if that's what the kid wants, I'm always glad because I know it's got a great infrastructure in place. But there is just as much joy, and sometimes more, to be had from other wishes as well.
If your son has specifics in mind, he does need to make sure his wish granters know them so they can make all the arrangements to make sure his vision is met.