How about a sport movie, with the Muppets forming either a basketball, baseball, or football team? Or maybe they can play a sport that doens't get as much movie exposure, like Golf, Tennis, or Bowling. It would probably be a challenge to have the Muppets actually play sports in a movie.
Or, considering how memorable that the bicycle scenes in the first two movies were, how about a Muppet bicycle movie? Maybe Kermit, Miss Piggy, and a few others could be involved in a bike race, or they could be riding their bikes one day and sudenly get involved in an adventure, needing to use their bikes? A variety of effects could be used (radio controlled Muppets on bikes, the old-fashioned marionette way, the way it was done in the Ford Hybrid commercial, blue screen technology, minimum computer-animated Mupepts). There aren't very many bicycle movies.
Or maybe a Muppet version of The Three Muskateers, with Kermit, Fozzie, and Gonzo in the lead. Or a Muppet version of The Prince and the Pauper (though Kermit would have to portray a child, unless a human plays the title roles and Kermit only gets a supporting role).