there is quite a bit that has changed since 2000. Mission: Space opened in Epcot, as well as a complete makeover of the Living Seas. SSE is being refurbed as we speak. Soarin' was recently added. And El Rip del Tiempo was changed to the Gran Fiesta Tour. That's EPCOT, next up, Animal Kingdom...
DAK hasn't changed too much, besides Expedition Everest. Can't remember if the Chester and Hester's area of the Dinoland area was there in 2000, but it's there now. Oh, and there's the Finding Nemo musical where Tarzan Rocks used to be.
As for Magic Kingdom, there's Mickey's Philharmagic, the new Laugh Floor thing with Monster's Inc (Timekeeper, RIP

). Pirates was just recently upgraded, and HM id getting some much needed TLC right about now. Stitch's Great Escape would be a pass-over, replacing a much better version.
And, Finally, MGM. Not too much has changed here, the most stagnant of the parks. There's the
Lights, Motors, Action stunt show, the short
Journey into Narnia walkthrough, and the Walt Disney: One Man's Dream that they put in around the 100 Years of Magic celebration. Outside of that, about the only other thing was the randomization to Tower of Terror.
Whispering Canyon is still there, but as we didn;t eat there in December, can't confirm the horse or anything. Buzz is still in Tomorrowland which is always fun. As far as reccomendations, most of the changes are (IMHO) not-to-be-missed. But to each his (or her) own.
"And please do not sit on the floor. My studies show you can't experience time travel on the floor. and it's not a pretty picture in those shorts" - The Timekeeper
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