Personally, I think muppet cameos would be distracting. Very distracting. Story is king when it comes to movies. You should have fun while making it, but bear in mind how an audience will react. Some may giggle and find a muppet cameo funny, but to others it may seem tired and unnecessary. I've worked for Dreamworks, Sony, Nickelodeon, Cartoon network, and others. And the temptation to put little jokes and cameos like that in a film or series is a constant. But, if you depend too heavily on that, you lose sight of what makes a show special on it's own rights. My personal opinion, is that it cheapens the story. Fraggle Rock never had to depend on hip cultural references to be cool. It just was.
Oh, and yes, to get the other muppets, Henson would have to negotiate with DISNEY *groan* They basically destroyed their own animation company, so wait and see what they do with our beloved muppets.