Here's more of a general idea on how to rework some things in the area of the Motor Boat Cruise and the monstrosity that is the current Autopia.
I would move the Autopia over to the old Motor Boat Cruise area and make it an indoor/outdoor fantasy dark ride, themed to what, I don't know. You would still have control of your vehicle like in Autopia - being a kid once, I know how much fun this is for them.
The Motor Boat Cruise loading dock and surrounding water would be a lagoon and queue area. The queue would take you under both Monorail tracks, which would therefore not have to be realigned .
The two level show building for this ride would be in the area inside the second loop of the Monorail, where most of the Motor Boat Cruise and old Fantasyland Autopia loading area were.
Some of the existing Autopia track just to the east would be used in the new ride. Additionally, the roof of the show building could have outdoor track.
The PeopleMover track in that area would be rebuilt and realigned to go through the middle of the new show building.
The pathway from Matterhorn to IASW would be straightened a bit so you can see the full IASW facade as you walk towards it.
The massive space of the current Autopia loading area would be freed up for a new attraction. I'm not sure how far east the underground part of Submarine Voyage/Nemo goes, but conceivably that eastern sliver of land could be used as a show building for the new attraction being installed here.
What does this accomplish?
1) The non-futuristic Autopia is removed from Tomorrowland.
2) Space is freed up for a true futuristic attraction.
3) A self-steering attraction (similar to Autopia) is rethemed to Fantasyland.
4) No construction necessary on top of Nemo.
5) Monorail would not have to be touched.