Teebin is a great source for what was *supposed* to happen with many of the elements in Forbidden Journey - many of what I'm about to list comes from posts from him and other sources. If he'd like, he's more than welcome to share or correct any of the following.
Off the top of my head...
-As we all know, the Floo Network projection was changed a few years into the ride's operation
-Dragon's original intended motion (perhaps seen in testing and in the opening weeks, I wasn't there so can't confirm) was more dynamic, with the dragon swinging his head & neck more and clearly lurching its jaw forward to belch. If someone can find the tech demo video from Entech, it'll show the original intended motion
-Aragog was supposed to move in some capacity and not be a stationary prop (not sure if this applied to the other spiders, or if they were always intended to be stationary)
-Whomping Willow scene was allegedly hit the hardest: was supposed to be much brighter, more dynamic effects, possibly (can't remember where I read this) more moving limbs... something got cut, so the lights were turned down
-Dementors lost their hands due to WB deeming them too scary (...)
-There was supposed to be a horde of dementors in the final moments before the third dome; this too was determined to be too scary by WB and the effect was turned off. The dementors are still there, turned off in the darkness, can occasionally be seen (apparently now better than before due to increased dome brightness). One of them still has their hands, as pointed out in a recent breakdown video
-Perhaps most significantly - entire ride was supposed to be in 3D and the CGI was produced as such. The long Sorting Hat hallway is where we would've retrieved our 3D glasses. This was cut for multiple reasons (motion sickness concerns? glasses falling off?)
That's all I know of. Again, I'm not an authority on this, just recalling what I've read on here and other places.