John IS very much involved with all aspects of the Comapny along with Steve Jobs. It looks as though Even is Iger is sitting in the chair, the two of them are actually running things creatively. The results of their short time there are already begining to show, (the Nemo attractions) and the next year things should explode-IF they are given the tools, personal and money to do what they want, and that will depend on the success of the films they are involved with.
There already is a Muppet connection with Frank Oz and Karen Prell, so anything is still possible with a Henson/Pixar combo, but nothing has been said. The Muppet animatronics for California Adventure is a small start, but there is also talk of removing MuppetVison all together, so it's hard top say just how important the characters are to Disney in general.
My feeling is that unless this Fraggle movie or DK2 do well, they will just keep selling dolls and DVD's until they get their money back on Eisner's ego buy, then cut them loose, effectivly anything great coming from the Muppets ever again.