An Electric Mayhem movie (or even TV special or direct-to-video production) could be a hoot. They're a more cohesive unit, from both a comedic and musical perspective, now that the recasts have settled in.
I would even suggest a Behind The Music type of faux-documentary if Robot Chicken hadn't already used that format - obviously it would have a MUCH different tone than the Robot Chicken piece, although I must admit I found parts of that to be pretty funny.
But I'd be curious to see a full-length Muppet production (movie, TV-movie, TV special, direct-to-video, whatever) that only concentrates on one character, or a small handful of characters, and doesn't try to cram as many Muppets into the mix as possible. Not a kiddie-driven KSY type of thing (although I do love parts of KSY) but a serious attempt to develop an engaging story for one or two Muppets.
I know we've enjoyed seeing so many of our old friends in the two newest movies but one of the things I like(d) the most about TMM is that the main players got a little breathing room. Sure, you had the Mayhem scenes, the soundstage finale and the big Muppet mob shot at the end, but for the most part it was just two or three Muppets at a time. I think it allowed them to become richer and fuller as a result.
And if any one Muppet ever got to anchor his own "story," I would love to see that happen to one of two very different characters - Pepe or Rowlf. I think Bill Baretta is doing wonderful things with both of these characters, has proven that they work beyond supporting roles (at least in small doses in TV interviews, ads and online) and that they each command an audience that exists outside the usual Muppet dynamic of Kermit-Piggy-Fozzie-Animal. And Baretta has a terrific singing voice for both of these guys, too.
Seriously, I think a Pepe movie could be amazing. Imagine a prequel that followed his life before the Muppets and ended with him joining the cast of Muppets Tonight. Or even his own separate adventure that didn't rely whatsoever on Muppet canon. I think that would be a marvelous challenge for any screenwriter (and I suspect that any combination of Stoller, Bobin, Lewis or Thatcher might relish that challenge).