I'm trying to remember what my younger cousin liked a few years ago.
MK - All of Fantasyland, Tiki Room, Country Bear Jamboree
Epcot - Honestly, I think 3 1/2 is a little young to even fully enjoy something like Turtle Talk, but I'd go with that one and Journey into Your Imagination. Plus, he liked making the masks in World Showcase, but that got old after a little bit.
MGM - Muppet 3D, Voyage of the Little Mermaid, Playhouse Disney, Beauty and the Beast Show, Honey, I Shrunk the Kids Playground
AK - Safari, Lion King Show, the various trails (It's Tough to Be a Bug was a little scary for him)