My gut reaction is that this is a bad idea, and I hope the rumor turns out to be false. But it seems that in the world of theme park management, bad ideas are the very ones that sometimes really take hold when they're trying to prove how ground-breaking they can be.
Muppet*Vision 3-D works. It worked in 1991 when I saw it for the first time, and it worked in 2007 the next time I saw it. My kids loved it, and my theme-park-novice wife was firmly convinced (after the previous interactive effects like Fozzie's squirting flower) that the remote control banana creme pie was about to be dumped all over us.
(Who can blame her? The day before, at the Magic Kingdom, we happened to pick the very two seats that the animatronic Stitch expectorates on!)
What I wish is that 'Here Come the Muppets' had still been running for my kids to see. Sigh... someone start a campaign to bring back a show like that, but with better puppet/costume technology. The human-sized walkaround Muppet costumes from back then were a novel 'ice capades' approach, a quick way to get Muppet content into the Parks while MV3D was being completed, but ultimately I think that approach failed because it robbed the characters of their inherent puppet magic.
Ironically, the show that replaced it, Voyage of the Little Mermaid, uses actual hand-puppets for several of the animated characters, with their performers dressed entirely in black and hidden from view. (I was videotaping it last August and switched my camcorder to infrared out of curiosity... but as soon as I saw a few seconds of the ghostly green outlines of the puppeteers capering and contorting, I flicked the switch again to make them once more invisible. I guess you truly can destroy the magic sometimes.)
That variation on the classic bunraku approach could work amazingly well with the existing soundtrack of HCTM. Build the 'stage floor' at knee-height of the black-clad puppeteers, with any of several possible techniques for making the puppets' legs walk, and real Muppets could walk and talk and do the show, seen head-to-toe.
Don't get me wrong, remoted controlled puppets like Bunsen and Beaker, from the Mobile Muppet Labs, are great and I think it's wonderful that Disney tried a new technology out with those characters. But I just think the Parks ought to embrace what makes the Muppets unique... the magic of a performer's hand inside, bringing a scrap of felt to life.
Another 3-D movie? Snore. Seeing a real-live Muppet Show? Who wouldn't want to see that!
Alex