My kids loved The Seas With Nemo and Friends at Epcot. The nice thing is that there are a lot of activities at the theme parks for kids, aside from rides and shows. Depending on the time of year, there are festivals and special attractions set up. (For example, during the spring Flower and Garden Festival at Epcot, you can visit the French perfume garden.)
At Epcot in the afternoon, go to each pavilion in the World Showcase. There is an area set aside with markers and a mask to decorate, that you then take to each country to get stamped. Don't forget Innoventions. There are play areas at Imagination and Mission: Space, as well. There are Behind the Seed tours of the greenhouses, and a jumping water fountain outside of Imagination. OOH! And the koi pond outside of the Japanese restaurant. Pretty much, with a little exploration, you can find a lot of things to do if your child is too young for certain rides.
At Animal Kingdom, the jungle trek and forest trail have a similar passport program. The kids can identify animal scents, follow a map and identify animals, and sometimes "earn" a fastpass for Kilimanjaro Safaris. Lots of hidden trails for exploring. There is also a bunch of caves built into the oasis, with a bouncy bridge and colorful parrots... or they can dig in the Boneyard. Rafiki's Planet Watch features a train ride, a conservation station with small animal exhibits, and hands-on activities.
At the Studios, a must-see attraction is Voyage of the Little Mermaid. Make sure to Fastpass it or get the first showing of the day, because it's popular. MuppetVision 3D is a lot of fun as well. My kids liked the Playhouse Disney show when they were younger. There is a Bug's Life-themed playground practically behind the Sci-Fi restaurant.
At the Magic Kingdom, there are spitting camels at Aladdin, tiki god statues that spray you near the Jungle Cruise, Pooh's Playful Spot, and Storytime with Belle. If your daughter loves princesses, walk through the castle between stage shows. There is a detailed Cinderella mosaic. Um... there is really a lot to do at Magic Kingdom for younger kids, and I know I'm forgetting something.