With respect, I really don't see how the Muppets can't be popular again if they're given the proper forum. There is something so human and timeless about them; Eisner bought them because he saw that, because he respected Jim, and because as said Disney was the logical place for them to go.
Like Mickey and Donald they have an iconic quality that makes it irrelevant about when they were actually conceived. They also bring a much-needed innocence, optimism but also wit to the harsher and more cynical place the world has become. It might be a different place from the time the deal began, but the Muppets are still the Muppets.
Pixar already knows how to cross over age barriers and make all kinds of concepts (Rats, disillusioned old men, 700-year old Robots) appealing to so many people. The Muppets are already so great, so how much of a stretch can it be that they'll make them popular again? If they can make a sequel to a film that hasn't been in theaters for eleven years a critical and commercial hit, they can do this.
Also, one thing I think people have forgotten, or at least haven't considered, is....Sesame Street! It's still quite popular; not only that, there's still kids' clothes and toys inspired by the characters from that show. And they ARE Muppets. True, Disney can't market them as they don't own them, but the fact that kids still love Ernie and Bert--a classic Henson/Oz pairing--very much suggests that there's hope for the rest of the Muppets.
The Street's Muppet website:
http://www.sesamestreet.org/muppet

You can’t just have your characters announce how they feel! That makes me feel angry!