My 3yo nephew had a blast in Epcot! Oddly enough, more so in WS than FW (he's affraid of most rides). But in FW, he did the cookie baking thing in the Food Pavilion, and he loved Living Seas and he liked a lot of the educational displays at all the other pavilions.
In WS, he loved the model trains outside of Germany. He didn't do either of these, but I know the have Kidcot stations were the make masks at each country, and you can buy a "passport" that they can get staped at each country, too. He liked lunch in Mexico at the San Angel Inn, and loved looking at all the "neat" stuff in all the shops of the World, as well as the entertainers.
Mainly, he just loved spending time with his family!