The 90's weren't all that bad, the problem was the company wasn't sure what to do.
As Gonzo said, we lost two MAJOR performers, one who was the head of the compnay and the performer of a lot of major characters. The company didn't know what to do at all. They had lost many characters such as Rowlf, Dr. Teeth, News Man, Sweetums, Scooter, Janice, ect. I mean, thats a lot to lose. Also, characters like Kermit had to be taken over by a totally new performer, who does a great job, but had to learn to be a character really fast.
Not only had 2 performers been lost, but one went on to do other things. Frank Oz became busy and started to have less and less to do with the muppets. In MCC Fozzie was baerly (get it?). Basically, all of his characters had small parts. In MTI Frank was back, and it was great. Too bad it didn;t stay that way. In MFS, he was gone again, only doing voice loops. It's just wasn't the same.
Now lets not forget MT. That was a show that tried to go in a new direction, but didn't work out well. It was to many new characters at once, without enough old characters. Sure we had Kermit, Gonzo, and Rizzo is just about every episode, but most of the time Piggy wasn't in the show. Fozzie showed up once in a blue moon. There was just an absence of the characters we know.
So, the 90's were a hard time for the muppets because of so much bad stuff that happened. Frankly, I too am surprised any movies were done, yet we got 3 and a TV show, even though it was short lived. I mean, that was pretty good. Fortunatly, we now have a formula that works. A good mix of classic and new characters that compliment each other. New performers that are taking on some much needed characters. It's really a much better start now than it was in the 90's.