Having just discovered this thread, I have thought of a few ideas as well, in addition to these great ideas:
1.) A music shop where you are greeted by costumed versions of the Electric Mayhem, and you can pick albums and CDs of all the great Muppet songs
2.) Baby Piggy's Dollhouse - A larger-than-life-size version of the dollhouse used by Piggy on the Muppet Babies. You can even greet costumed versions of the babies themeselves, including Skeeter!
3.) Tutter's Mouse Hole - For the small-fry, it's a tiny rollercoaster that lets you go into Tutter's home in the Big Blue House, as well as the kitchen. Tutter then appears at the end as your kids get off the ride, wanting to take a picture with you.
4.) An international exhibit - You're greeted by several international Muppets depending on the theme of the country (i.e. Abelardo Montoya for Mexico, Mopatop for the UK, Pino for Holland, Max Mekker for Norway, and Kippi Ben Kippod for Israel)
5.) A live stage where the Muppeteers come on stage to demonstrate their characters. Even the cartoon voice actors associated with Henson's cartoons (namely Muppet Babies) appear to take questions as well.
6.) Doozer Kingdom - Similar to Tom Sawyer Island at Disneyland
7.) Digit's Arcade - Obviously, where you go to play video games
8.) An exhibit where you can greet the human actors from many Muppet shows, such as Gerry Parkes as Doc from Fraggle Rock, or even Jennifer Connelly as Sarah from Labyrinth!
9.) The Cave of Dinosaurs - You are greeted by many characters from Dinosaurs, like Earl, Fran, Robbie, Charlene, and the Baby (Gotta love him!).
That's about it.