To be fair, I've been a Muppet fan my whole life, but had no idea who Uncle Deadly was until 2003 or 2004. He's not exactly the first Muppet to come to mind, and has never been in a Muppet movie prominently.
It seems that since James Bobin was so keen to suggest Uncle Deadly, it's very likely he found some places to add Scooter (and Pepe and others) to the script.
Brian said in an interview recently that he wouldn't be in it. He would consult, but not perform. Very sad, since Johnny and Sal were the funniest act to come out of Muppets Tonight, I think. Perhaps with the exception of Bobo.