Interesting question! Definitely not Nicky Holiday since he does have feelings for Piggy despite his sleaziness, lol.
He just used her. He has members of his own species to fool around with. Come on... like he totally wasn't with any of those girls that were swiping the baseball Diamond.
But I'm going with Doc Hopper ONLY because he's the only villain that was seeing to kill one of the Muppets. Singer was similar in intent, but considering he's a government agent, even though what he was doing was for his own ego, he thought it was the right thing.
Similarly, there's also (while it doesn't count here) Miss Finch. She wasn't evil, she wasn't out to destroy Big Bird... she felt that what she was doing to him, putting him up with a standard family of his own kind (more or less), was the right thing to do. While Singer's interest in discovering aliens was part ego (going back to the fact that no one ever took him seriously), it was also due to him thinking he was doing the right thing. I really want to see more Muppet movies where they have an antagonist rather than a villain.
A villain is always evil. An antagonist doesn't have to be. Candice of Phineas and Ferb, Inspector Zenegata of Lupin III... not evil at all, but they cause some sort of aggression against their respective shows' protagonists.
Do you really count Scrooge as a villian?
He's sorta evil but he's not really a villian.
Scrooge is his own villain... his own worst enemy. Muppet or no Muppet, A Christmas Carol was all about what greed and the pursuit of wealth can do to even the nicest of people. Sure, he had some past emotional baggage too (that wasn't in this version of the story, or at least not stressed) as well... but his problems were mostly with the price of success. He then finds redemption in the end.