All great ideas, Im visualizing a map in my head.Fun thread. I have a lot of thoughts, and the overall change would be drastic. I may try to draft something up, but that will take time...
In short, I'd pick a lot up and not put a lot of it back down (i.e., gone would be all the Value resorts, all the Official Hotels at DTD, the town of Celebration, the speedway, some of the golf courses, etc.). WDW would be much less developed than it is today in order to preserve its uniqueness (the above would all go back to woods and wetlands) as opposed to suburban sprawl as typified by Orlando. While the asset of Disneyland is the proximity and convenience of being able to walk everywhere, the size of WDW is/was its asset, because, if planned well and not over-built, it can and should feel like a Place Apart.
In this imaginary scheme, there would be five Resort Areas (MK, EPCOT, Studios, AK and DTD), each with its own themed resorts, recreation and water park (some shared). A greatly expanded monorail system (maybe powered by a clean-energy plant as a nod to Walt's utopian vision) would mean any place on property could be reached via one or fewer monorail transfers (e.g Grand Floridian to TTC North, then transfer to the AK, DHS, or EPCOT-DTD Lines) or an alternative, unique method of transport.
Another "Seven Seas Lagoon" or larger-sized lake would go in south of EPCOT with hotels such as the Boardwalk and Y&B more spread out upon it. Maybe a Parisian hotel on the outside of International Gateway (as you mentioned it continues the theme) and a Xanadu (Hearst Castle-inspired) hotel near the Studios (Studios would be moved to where the PopCentury/AoA now sits and the nearby Waldorf and Bonnet Greek Resorts would be acquired and removed). Many WDW hotels would have special access (via boat or foot) to their home parks (e.g. AK Lodge to AK via "River boat to Harambe"). And the much faster, better Seven Seas Lagoon-style launches would replace the loud, fuming brain-jarring Friendships on the new, deeper lake.