I figured that Walter has picked up the go-fer position, and Scooter has finally been promoted to... assistant stage manager, I think? (Assuming stage manager is Kermit's official position.)
I do think that the next movie (if it is a movie and not a TV series, where everyone can have a turn in the spotlight) should find a plot that doesn't need Walter as a featured character. In fact they probably should have done that for the second movie (at the planning stage), but with MMW as it was, Walter was basically necessary to play that part in the story. The only other choice would have been Scooter - and he did play that part in the similar plot from the comics, so perhaps using him again would be a bit too repetitive.
(My personal theory is that - in the Muppet Show's version of reality - they made MMW as a dramatisation of the 'real' events in the comic book. So Scooter was too busy behind the scenes to play himself in the film, and got Walter to act his part.)