I'm glad they got rid of Honey I Shrunk the Audience. It was a campy play on a bad movie that Disney beat to death. I can appreciate those who enjoyed it because it was part of their childhood, but Captain EO was part of mine.
That being said...both movies were bad. Were it not for MJ (and his music) being in EO, it would be a terrible show. It's sortof like Moonwalker...terrible movie, but for the music / dancing.
What I think is more important then the 3D show, though, is the state of the Imagination Pavilion as a whole. Journey has been ruined, Dreamfinder/Figment walkaround has been retired, the rainbow tunnel is no more (or at least, it's upstairs rotting). That whole pavilion needs a revamp. Until they are willing to do it right and with passion, I think they should pretty much leave well enough alone for the time being.