My only criticism of Muppets is the extremely irritating character "Waldo". However, that's nothing compared to the irritating pneumatic chairs in Shrek. During the chase scenes, the theater sounds like a giant compressor.
Muppetvision is still the best!
The chair movement was annoying. Not sure if the story in Shrek is non-canon or not. I stopped liking Shrek after the 2nd one came out as the animation was too herky jerky for me when they did action, and the jokes were typical Mike Myers. (I thought he was hilarious in the past, but he seemed to recycle jokes.) I've only been to the Shrek show twice and it never got better.
Muppets win for me... they are timeless, the show has charm, and can be enjoyed by anyone, and there aren't very many pop culture references. I think pop culture references work as long as they're updated constantly like in live shows, or in tv shows.
Muppets may be empty compared to Shrek, but there really isn't much to do in USH... the park can be done almost 100% in one day.
As much as I didn't care for the Transformers sequel (that opens a can of worms!), I hope the ride is similar to what I've seen about Spider-Man! And the Studio Tour is a part of history that should never be taken away... and I'm anxious to see what's been done to the new King Kong. And yes, Waterworld if phenomenal in terms of a stunt show... blows away the Indy one in Florida.
Yes, the Mummy at USF is a great ride, and much better than the west coast version, from what I hear. And Jurassic Park is really good too, after it got refurbished and the dinosaur AAs put back in working order.
As for Shrek 4-D, I've only seen it once, but I thought it was a fun show. The Muppets is much more charming, though. No contest.