It wasn't that Cranium Command wasn't very popular. It's the fact that after Metlife dropped their sponsor, Disney barely recognized the pavilion that it was in, and they never updated anything in there. ANYthing. NOTHING changed. Also the pavilion kind of became hidden behind trees in the back.
If you think about it too, if you don't know anything about Cranium Command... The name "Cranium Command" doesn't really grab your attention all that much. You'd think it's just some interactive game by the title and description, or some cheesy stage show.
It was by far one of the best attractions EPCOT has ever offered. It was timeless. It could have been popular. The problem was it's location, and where it ended up.