Greg the Bunny was a completely different concept, a sitcom on Fox, not associated with the Muppets whatsoever.
On Greg the Bunny, "puppets" were considered a real species. Living, breathing individuals not controlled by anyone.
I think that its safe to say that in this upcoming movie, the Muppets are real beings.
That is, Kermit is a real frog, Fozzie is a real bear, and so on, same as they have always been.
Despite the little in-joke of "don't look down" and such, in general the Muppets have always been considered real living, breathing, individuals. They are not puppets, they are real, and have occasionally been recognized as celebrities. Like in "VMMCM"
And I'm sure that they will no doubt continue that.