With all do respect, every single time I went to Hollywood Studios over the past 4 years, The Muppets was empty! Indy on the other hand is continually packed. The kicker is that the Muppets is also indoors away from the heat, making for an even more appealing target during the summer months.
Not saying that honoring Jim Henson and keeping the attraction is a bad move. But, Indy is a far bigger people eater show from what I've seen over my past 6 visits (granted this is from what I've seen). Despite it running continuously instead of 6 or 7 times like Indy, every Muppets show I've been to (be it October or June) has a theater that isn't even 1/3 full.
I hope they keep both honestly. I just think that it isn't quite the hit Indy has been and still is. Even Muppets Most Wanted under-performed in the US making only $50 mil.