Here's what I'm thinking. There seemed to be a lot of the original concept that Muppets Studio suggested the writer into going a slightly different direction. Not meddled, not violated creative vision for... just suggested. However, Count.... there were a LOT more acts that auditioned... and for spoiler's sake....
Johnny and Sal
Mr. Poodlepants
Clifford (appeared in one pannel standing nest to the piano)
Angus the Gargling Gargoyle
Mahnah Mahnah
Marvin Suggs
The Jughuggers
Wayne and Wanda
Bobby Benson and 3 babies
Geri and the Atrics
Dead Tom
So, I'm guessing that something may just be up with the Jim Henson Hour characters, though I'm not sure what exactly the ownership policy on them is. Still wonder who the heck owns Beautiful Day myself.
I also vaguely remember that Animal was supposed to keep sneezing every so often. but I guess that was changed.
But those are basically trifles for me. I'm loving this series, possibly even more than King Arthur... and that was my favorite.