Last night I thought it might be interesting for there to be a Muppet game where the bosses are all characters who weren't seen much. Characters like Mahna Mahna, Marvin Suggs, Angus McGonacle, Fleet Scribbler, Uncle Deadley, and J.P. Grosse. I was thinking J.P. could be a final boss, but then I can't really think of what he could do that'd make sense. While he was mean, it was mostly out of greediness. He wasn't really a villian, and didn't have any evil traits. Fleet Scribbler would also be a bit hard to figure out, but I'm thinking maybe a level where he follows you around, and you have to avoid him until the end of the level... He just chases you around, and you start losing energy when he gets close enough to you... Then you get to what is called a "safe zone", where you go behind glass, pull a lever, and a safe falls on him.
But most of the others could work well. While Mahna Mahna doesn't seem to be evil, he could work as a boss. Put him in a level where he's just wildly running and hopping around, picking up small objects to throw at you (which you, in turn, could pick up and throw back). Maybe the Snowths could be there, pulling levers that provide the objects.
Marvin Suggs could try to hit you with his mallet, and at times throw Muppaphones at you, which you could catch/ pick up and throw at him.
Angus McGonacle could use gargling powers to defeat you... Maybe smoke bombs can come out of his mouth when gargling.
I think that anything can work well for Uncle Deadley... Maybe he'd be a better final boss than J.P. Grosse.
Heck, the old gypsy lady and the aliens from the Jonathan Winters episode coudl also be characters to battle.
Then again, maybe it could just be a typical fighting game, like Mortal Kombat. J.P. Grosse can threaten to close the theater, unless the Muppets put on a fight. J.P. chooses people for the main characters to fight (the characters mentioned above), and the main characters have to win all battles to keep the theater.
Another idea could be a game in which Fozzie Bear spends the night in a haunted house, and has to fight off ghosts and monsters, perhaps by throwing tomatos and pies at them. It could have be in 1930s/1940s/1950s comedy style. A duo comedy game involving Fozzie would also be good... Maybe pair him with either Kermit, Gonzo, Rowlf, or Scooter.