2 ideas: Tron and a Weather Pavilion. The Weather Pavilion would have Stormrider cloned from Tokyo Disneysea as it's anchor to replace Body Wars. Stormstruck would be re-located from Innoventions into this new pavilion to replace the Making of Me. As for Cranium Command's location, not really sure what to replace it with, but a cool interactive weather show would be interesting. The pavilion's structure would remain the same, but the interior theme would be now weather themed. The Weather Channel or The Home Depot would be good sponsorship choices.
Tron would involve a complete gutting or demolishment of the building. The attraction would be a high speed dark ride where guests board modified lightcycles and venture into the world of Tron in order to eliminate a virus that is destroying the cyber world. Guests would enter Flynn's Arcade, walk past the dusty old arcade games and enter a secret hidden room behind the machine for his prized video game creation: Tron. There, Sam Flynn (Garrett Hedlund), would brief you on how he got trapped in the world of Tron, just as his father did and how you will be. You are then zapped by a laser and transported into the world of Tron, where you will board your vehicle.
During the ride, you will enter the grid in the middle of a lightcycle race, travel across the grid, though a city metropolis and all the way to an exit point where you destroy the virus and escape back to the real world.
After your journey and you are transported back into the real world, you return to Flynn's, this time not as run down and featuring exhibits about computers and how they have changed our world forever. The pavilion would be sponsored by Microsoft.
Those are my two ideas.