My son just turned 3, and here is his list of must-dos for each park (we are APs a couple hrs away, so he has been a ton... and is very opinionated):
DHS
-Disney Jr show
-Eat at Sci-Fi (bc you get to eat in cars)
That's about it. There's height restriction rides and shows, and he doesn't do well with sitting still. If your son is familiar with Star Wars, you can meet Chewbacca and BB-8 (skip Kylo Ren) or build your own light saber as a souvenir. Frozen Sing-a-long is also good for the whole family.
Epcot
-Rides: Frozen, Spaceship Earth, Living with the Land (mine doesn't love The Seas with Nemo or Journey into Imagination, but yours probably will).
-Play areas: There are tons of places for him to stretch his legs: The aquariums at The Seas, Imageworks after Journey into Imagination, the real cars to sit in after Test Track (can enter all these through the ride exits). He top two, though, are the hedge maze in the back of the UK pavilion and watching the miniature trains at the Germany pavilion.
-Getting little sodas: at Club Cool, there are little cups to sample sodas from around the world. He doesn't drink soda at home, so this is a Disney treat.
-Garden Grill is a good character meal option with Mickey, Pluto, Chip and Dale.
Animal Kingdom
-Kilimanjaro Safaris
-Triceratops Spin (a Dino version of Dumbo)
-Wildlife Express Train/Rafikis Planet Watch/Affection Section - you take a train ride and then can brush the goats in the Affection Section. Doc is also meeting there now.
-The Boneyard - Awesome playground with slides, etc. Make sure you go across the bridge that goes over the walkway - there is "the dig," which is basically a giant sandbox with buckets and shovels. It's coarser than sand, so easy to brush off, and its shaded with big fans.
-Tusker House is one of our favorite character meals with Mickey, Goofy, Donald and Daisy
Magic Kingdom
Here there are so many ride options, but here are my son's favorites:
-Dumbo
-Tomorrowland Speedway
-Tea Cups
-Barnstormer
-Small World
-Carrousel
-Jungle Cruise
-Peter Pan
-Walt Disney World Railroad
*Don't miss meeting Mickey at Town Square (he talks) and the Festival of Fantasy parade. We get Mickey ice cream bars while we wait.
-Winnie the Pooh is also good for that age, but mine decided he doesn't like it bc there is this super quick section with thunder and lightning (though he's not scared of real thunder and lightning??? It's a fun age...).
If your son likes fireworks, than all of the night time shows are great. Mine is going through a phase where he's scared of them though.