I agree. Captain EO was fantastic, but it would seem very dated and weird if they were still playing it today.
Having said that, even Honey I Shrunk The Audience seems dated today. HISTA was made in 1994, and it's 2009 now. So that movie is 15 years old!
Ideally, no 3D movie should run for any longer than 10 years. But Disney don't seem to be making as many of them as they used to, probably because 3D movies will soon be standard in normal cinemas, not in special custom-built theme park cinemas.
The most modern 3D movie made for a Disney Park is Mickey's PhilharMagic. But even that is 6 years old already. It opened at WDW's Magic Kingdom in 2003. In fact, Disney have only made two 3D movies for all of their theme parks, in this decade!