I wouldn't say that the Indiana Jones stunt show is in poor condition, it's just from a bygone era and a show that I've seen a half dozen times. Disney rides provide a physical sensation accompanied with visual things to explore. Shows, by nature, offer few to no physical sensations and the focus is more controlled, leaving less to discover visually on repeated viewings.
When I watch Muppet Vision, it feels incredibly 90's. The in-theatre effects are fun, but I would much prefer a new attraction that focused on practical real effects and physical puppets rather than watching a movie. Also, I think Honey I Shrunk the Audience finally fixed a problem I had with 3-D movies. I don't want to watch things jump off the screen, I want to feel like I'm in the same room with these characters. HISTA did this incredibly well and TTBAB was even better. With Muppets, it reminded me of the issues I had with the middle portion of T2 at Universal; I'm just watching a movie with 3-D effects in it.
In the end, Muppet Vision, already feels like a museum piece whenever I visit, and not much of a theme park experience. I am still charmed by the physical in-theatre effects and actor, but that's an extremely small portion of the experience. I'd rather have a new Muppet experience that feels fresh and new and incorporates physical gags and energy throughout. If they simply move Muppet Vision to another part of the park, I would be extremely disappointed.