Clifford really disappointed me as an emcee, and not just because he isn't Kermit. "Mmm, she sure is...wholesome." Clifford has the look but lacks the personality.
Pepe is also a horrid choice. I just think it would be nice to have a host who's not going to totally perv on female guest stars. I realize Kermit sometimes expressed his crushes but at least he was tasteful about it.
I kind of like the idea of Johnny and Sal, but they might wear out their welcome. To avoid this, why couldn't the duty be shared by multiple Muppets? Either one or two Muppets get the opportunity to host an entire show
-OR-
Several Muppets share hosting duties for every show. Maybe Fozzie comes out and does a monologue, Kermit, Sam and Rowlf could do talk spots, Bunsen and Beaker could introduce musical numbers, etc.
If there had to be one character to emcee, though, my top three choices would be:
Kermit
Gonzo
Rowlf