It was first changed back around 2000 to update the ride and to get rid of Figment (rumor had it Eisner never liked Figment, despite the fact that he outsold Mickey in Epcot). Eisner announced at the stockholders meeting in Chicago that year that Figment had gone to "Figment heaven." (at the same time claiming to miss Figment himself)
The replacement ride frightened quite a few kids and received a lot of bad guest comments from what I read (deservedly so).
They redid the ride, injecting back in as much Figment as possible to make the ride that exists today. It's still more similar to the replacementride (JIYI) than it is to the original ride, albeit with Figment.