I hope that Pepe continues to be a main character after the new movie. Rizzo, too. Though I seem to notice a trend when it comes to the Muppets Tonight characters being integrated with the classic characters.
At first, the Muppets Tonight characters who continued to be used were Pepe, Clifford, Johnny Fiama, Sal, Bobo, and to a lesser extent Dr. Phil Van Neuter. Then Clifford and Dr. Phil were pretty much dropped, and it seems that Bobo was retired for a few years. Then after The Muppets Wizard of Oz Johnny and Sal were very scarcely used, and around 2008 they brought back Carl (who hadn't been seen since Muppets Tonight got canceled) and Bobo, and it seems Pepe, Bobo, and Carl had become "the Muppets Tonight three" to be used with the classic characters (Andy and Randy were also brought back for one episode of The Muppets Kitchen). With the new movie, Bobo is the only one to be a major character, while others are included.
If they drop Pepe, then Bill Barretta will be able to focus more on Rowlf, Dr. Teeth, and The Swedish Chef, but I hope Pepe will return as a main character in the next big production after The Muppets.
Maybe this belongs in another thread, but while Henson and Disney have been recasting many characters originated by Henson, Oz, Hunt, and Nelson in the past decade (some characters changing hands throughout the decade), it seems they don't want to recast Clifford or Sal. I don't know if they just think people won't care about them as much as the classics, or if they are holding out hope they can eventually get Kevin Clash or Brian Henson to perform with the Muppets again someday, or if it's something else (Bill Barretta might not feel too comfortable performing Johnny Fiama to anyone else's Sal).