The sci-fi third gate concept as I see it:
Layout: based on Tokyo Disney Sea with a hotel entry complex and central lagoon with the "lands" radiating around.
First act: Discovery Bay, based on the original concept devised for Disneyland, is a fitting opening sequence for this park as the theme is built upon the pioneers of science fiction: Jules Verne and H.G. Wells. Fully built out around the central lagoon, there are plenty of opportunities for the basic "Main Street" functions, not to mention an air of nostalgia. Additionally, the layout around the lagoon would provide the opportunity to develop sub-areas (like a version of Disney Sea's Mysterious Island, etc.) for attractions and expanded theming. The hotel complex would carry this "old" sci-fi theme as well.
Lands: Themed lands based on the various Disney-owned properties would ring the outer edge of the park, radiating out from the central point of Discovery Bay.
I envision three basic concepts, but there could certainly be others (not to mention expansions based on future concepts). By the way, these aren't necessarily the "names" of the lands...that part needs more work.
1.) A Galaxy Far, Far Away. The worlds of Star Wars provide ample material for Imagineers to run wild... I see it as a sort of Star Wars "World Showcase" with themed areas bringing various locations from the movies to life.
2.) Pandora. Disney needs to get some mileage out of the Avatar deal, and while it isn't an overly popular concept among Disney-philes, I think it certainly fits a lot better in a sci-fi theme park than it does at DAK. In my mind, this is the smallest of the lands, but there is plenty of room to make something impressive.
3.) Mutants and Heroes. A take on an alternate version of the world as we know it, the Marvel universe. But I wouldn't stop at Marvel, how about an attraction themed to The Incredibles?
Of course, there are other, ahem, less popular Disney sci-fi properties...Treasure Planet, John Carter, The Black Hole, just to name a few. But really, to me there is a lot of room to create something different from the other parks, to really take these newer acquisitions to a higher level. Who's with me?!