I wonder if the movie will have any puppets that were used before the sale of the Muppets (as opposed to having everyone rebuilt either recently or for the movie). I would expect many of the puppets used on Muppets Tonight to still be in good use (especially those who haven't been used since).
Somebody mentioned the Houses, and somehow I don't know how they would work, unless they made a Houses sketch like on the show.
Considering it'll have "every Muppet you can think of", I think it's safe to say that, even if it doesn't have every character we can think of (I wonder if Jason Segal will get fan mail pointing out any absent character), it should have any Muppet used within the last 3-5 years.
And depending on how many characters were rebuilt for this (obviously Thog and most likely Uncle Deadley, but who else?), I hope Disney finds ways to continue using all newly-rebuilt minor Muppets.