Whilst a 3yo will get enjoyment from both parks mentioned, I would probably go for Seaworld myself rather than the other parks.
If I had to choose between Universal Studios and Hollywood Studios, I think the Disney Park just has that bit of an edge for a 3yo, but only just!
My DD at 2 loved the Lights Action Motors stunt show. There is the bugs life playground, Playhouse Disney, Little Mermaid Show, Muppet Show, Beauty and the Beast Show and the Fantasmic show. If your 3yo likes little Einsteins, s/he can meet them either as a charater greet or they have a character breakfast.
Universal Studios has Barney which DD loves. A great Fivels play area, ET, a animal trainer show, Curous George's playground (take a change of clothes!!!). There are characters too: Curious George, the animals of Madagascar, Scooby, Woody Woodpecker, Zorro, Barney,. Jimmy Neutron and Shrek shows are OK but can get a little scary for a 3yo. Most of the other rides/shows are too intense for most 3yos (Jaws, Twister, Earthquake/Disaster).
-Kay