Everybody who says IO should go in Cranium Command's spot either:
1) Hasn't seen the movie yet
2) Has never actually physically done CC
Inside Out much, much closer to the original iteriation of "Journey into Imagination" than "Cranium Command". Pete Docter even did an interview recently with the Disney blog who questioned him about it. He worked on CC's animation when he was an intern with WDFA, and remembered it about a year into making IO. He initially thought, "This is exactly like Cranium Command!" and then said it ended up "not even being close". And, well I agree with him.
Not only do the emotions never deal with any body functions, but Headquarters looks NOTHING like the CC theater, which by the way was tiny and only sat 200 people at best. Even if you drastically changed the set, and added animatronics of the emotions, which btw would face away from the audience, you'd be ignoring Inside Out's best aspect: we rarely looked at Riley's POV (the basic centerpiece of Cranium Command), but instead the filmmakers were much more focused on what was behind that, the world of her mind.
The entire Imaginationland sequence and Dream Productions felt so much like the original JII that they even threw in a Figment cameo in there. (fittingly enough, as a doll on a pile of rubble) The movie also has "the train of thought" that runs thru Riley's mind. The attraction writes itself.
So why would Disney struggle to get a pavilion back from festivities, one that which has been gutted and is rapidly aging, just to radically redo a tiny theater space that barely seats anyone as a use of their newly acquired hit Pixar IP when there is a perfect fit attraction just begging to be retired and replaced that would work so much better?
Imagine walking into Riley's mind... navigating the corridors of Long Term Memory as the switchbacks. A mind worker AA (which would be insanely easy to make) talks to guests, sets up the world and maybe is interactive while you wait. Then maybe a Headquarters pre-show using pepper's ghost with the emotions (who are very animated and cartoony), and then you get whisked away through Riley's mind via the train of thought and visit all the personality islands, Imaginationland (which COULD have an appearance by Figment and Dreamfinder), and Dream Productions. They could revive the Image Works upstairs to be a Headquarters you can interact with, with lots of IO-related interactive exhibits. The possibilities are endless with this IP and this pavilion.
And I know people are sick of Pixar, but if you've seen the movie, you would want this too. Inside Out is amazing... way better than Frozen.