K. Edgar Singer was much too silly to take as a serious "evil villain" even if was wanting to cause harm to Gonzo. Nicky Hoilday was a threat for sorts for Miss. Piggy, but not so much as the Muppets to a whole, since he just wanted to steal the Baseball diamond.
Like I said I can't classify Singer as a villain, as what he's doing isn't really evil. Egotistical, sure, but he's doing what he thinks is right. It all comes down to antagonist vs villain. Sometimes the villain is the protagonist, sometimes a good guy is an antagonist.
On that note... I love how the antagonist in MTM isn't even a physical being! It shows that you don't even need a "bad guy" to come in and give the heroes a hard time. It was all about the struggles of trying to make it big. Failure was the antagonist.
So for me I'm thinking between Doc Hopper, Rachel Bittermen, or Tex Richman. All were acted and did what they did out of greed, so it's hard to really make a choice between those three. It's a hard choice, but I think I'm going with Doc Hopper, cause he did hire someone to cause harm to Kermit if he didn't agree to be his mascot. Yeah Tex Richman wanted to own the Muppets studio and name which makes him pretty bad, but he didn't set out to harm a Muppet or possibly kill one.
Yeah, Doc was far more concerned about getting his own way and winning. It wasn't fueled just by greed, but by his own personal vendetta and achieving what he feels he's entitled to. Somehow, I'd feel Doc would find another singing frog, one with out any scruples that would do anything for money... but he wants THAT specific frog. And it doesn't matter if he wanted Kermit to sell his species out, he wanted to kill Kermit for refusing him. That's a very psychotic true evil. Rachel and Tex would've tossed them out on the street... sure, they'd probably find a way to bounce back in time (in the case of The Muppets, they'd just change their name and start over)... but Doc's killing of Kermit would have stopped the movement right there. So there's a greater instance of urgency. Of course, even cutting out the cut sequence where Tex had a reason for hating the Muppets, he was the only one in the group that actually changed in the end (Bowling Ball injury or not)... both Doc and Rachel stormed off (or in Doc's case, running away), ending up empty handed and getting what they deserve. Tex seems to come out of the movie in the end a nice (though brain traumatized) guy.