I wonder if Scooter could have played Jim Hawkins, if Richard Hunt had been alive or if Scooter'd been recast by then. Though part of me also feels he could have played Mr. Arrow.
I remember a friend mentioned this idea to me a couple years ago and when I first read it, I instantly fell in love with it. Granted, I may sound a little biased since Scooter is my favourite muppet and I know there are probably going to be some people who will disagree but I really do feel he would've been perfect for the part of Jim Hawkins.
I do wonder myself if this could've happened if Richard had been alive or Scooter were permanently recast at the time. But I do think there could've been a good chance, if they were looking for a muppet character to play Jim Hawkins instead of a human. Also, considering the loyalty Scooter (usually) shows to Kermit and in the film the character Jim, in some way having to decide if his loyalties should lie with either Smollett (Kermit) or Long John Silver, I think is another reason Scooter would've been good in the role.
Plus - for me personally anyway - it would've been so much fun to see the chemistry between Scooter, Gonzo and Rizzo and have them as the main three characters in the film.
But I do also like your idea of Scooter as Mr. Arrow, minor muppetz. Just imagine him kicking butt like Sam did towards the end of the film! haha