It'll be interesting to see where a third film goes. I can't see Bobin coming back, since he has that Alice in Wonderland sequel due for 2016, and any Muppets sequel will likely be out either then or the year after. Not sure if Stoller would come back for writing, but I'd enjoy a fresh team this go around.
I think it'd be interesting to see the Muppets actually in Hollywood and trying to get a movie made. Kinda like a self-aware "making of" the actual film.