There are a lot of options here, so I'll just pick five where I feel like the park suffers the most from losing them:
Great Movie Ride: The Runaway Railway may be great, but it could have gone in another place.
Horizons: Mission: Space is fine, but Horizons represented the soul of Epcot more than any other attraction.
Mr. Toad: Its madcap fun is missing from Fantasyland. Pooh is okay but lacks that same energy.
The Skyway: I understand why it went away, but it really helped with the "world on the move" idea of Tomorrowland and added an extra layer to Fantasyland.
Journey Into Imagination: One of the true gems and the type of attraction that could still be timeless today.