That sounds so fun for a toddler birthday! Maybe a character meal, if he likes the characters? Sometimes little ones are kinda scared of them but sometimes they are just all about the characters. Goofy's Kitchen might be a lot of fun, or the Stitch breakfast over at Paradise Pier. Or breakfast at the Plaza with Minnie and Friends-- the most characters.
3 days is probably good, though I kind of prefer 3 full days with a half day on one or both ends. Like, we're coming in on a Wednesday and going to the parks probably midday. Then 3 full days. Then a morning before we fly out at 3 p.m. But your 3 days might be just right for your little guy without overwhelming him. I second Jperiod's suggestion of naps-- I believe that at any age, everybody does better when you ditch the parks midday when it's crowded, go back to your hotel, and get in a nap or rest, maybe a little splashing in the pool. Also, go with the flow, toddler speed. Stop and smell the flowers. Wave at Mickey. Shorter stroller naps can be awesome, while Mom and Dad have a glass of something reviving- maybe a margarita on the Wharf if you partake of such things.
Where are you staying? Adding you to the thread on the OP. Hope your trip is wonderful!