Perfect example: After Walt Disney died in the late 60s, his company didn't get its legs back until the very late 80s with the release of The Little Mermaid and their co-production of Who Framed Roger Rabbit. In those middle years, the Disney people didn't know what to do, floundering through a bunch of awkward productions (how many Herbie films do we really need?), and a couple of brave, yet meager successes (Something Wicked This Way Comes was their best and most original work since Walt's passing, and Return to Oz was in many ways better than it's MGM predacessor). But they eventually found their voice, managed to envoke some of the spirit of the old Disney magic and became a success again.
I think this could still happen for the Muppets, since they're following an eerily similar pattern: They were booming in their early days, rode rough waters in the post Jim years (add your own example here), and found moderate success in some productions (The Adventures of Pinocchio and Buddy were a lot cooler than people want to admit). By this pattern of logic, success for the Muppets is inevitable.
Of course, assuming that this seemingly shared chronology of success is all a lot of hooey, I still think the Muppets can pull it out of the fire. I've been an outspoken critic of a lot of the business that's been happening with them in recent years, but I can't allow myself to lose faith. So, like the rest of us, I'll do my best to be a loyal fan and just wait out the storm, anxious to catch the first glimpse of success on the horizon.