Some of my ideas might overlap with some already said but here is what I would do.
1. Indiana Jones Ride - my hope would be for a duplicate of the one in DL. I would also knock down the Backlot Express in order to make room for an extensive and well themed queue
2. Sounds Dangerous conversion into Star Wars themed restaurant. You could have several different themed eating areas inside the restaurant that were featured in the films. Mos Eisley Cantina, Couruscant, Naboo, just to name a few
3. Sci-Fi Theater moved to Sunset Boulevard. Since that area is for the older Hollywood era, I feel a black and white theater would fit the theming over there. Also, use the old Sci-Fi theater for a Lost exhibit, which fits because the ABC commissary is right next to it.
4. Beauty and the Beast stage show - I would remove this and replace it with something that fits better with the Sunset Boulevard, early Hollywood time frame. My idea would be a dark ride that takes you through all of Walt's early creations. Mickey, snow white, pinocchio, etc. The ride could conclude with the One man's dream exhibit and film.
5. Now that the One man's dream exhibit is out of "Pixar Place", the area can now be extended left and right of Toy Story Mania. I would combine the what used to be Narnia exhibit with One man's dream and have a Wall-E dark ride, or a dark ride from a future pixar film. Next to Toy Story Mania, a Monter's Inc doors coaster, which could also include the space currently taken up by the Backlot Pre-show. Then, convert the Honey I Shrunk the Kids to A Bug's Life and convert the Studio Catering Co. to a pixar themed restaurant. I'm not sure why Pizza Planet hasn't been moved to Pixar Place yet, so I would move pizza planet to that location, and convert the old pizza planet into an extension of the muppets area.
6. I would leave the Backlot tour. I think adding a Cars Land to Hollywood Studios is overkill. It should remain in DCA. The only thing I would remove from the Backlot Tour is the Pre-show. Pearl Harbor is an old movie and that area could be used for an awesome monster's inc coaster. I also think a Ratatouille restaurant is overkill, since France is like a mile away in Epcot, so I wouldn't include that in the Pixar Place expansion. Plus, leaving the Backlot tour means you get to keep the streets of america, because their purpose is for the Backlot tour ride.
7. I don't like to see empty space, and there is a theater behind the streets of america that used to house the hunchback of notre dame stage show. Maybe it could be part of the extension of Pixar Place? With an Up show or Incredibles show in it?
Even though a lot of these things require moving places around, mostly all of the sturctures are there. The only sturctures disney would have to build would be Indiana Jones, Monster's Inc, and the new Sci-Fi theater. Then they would just enclose the Beauty and the beast area, with maybe a little extension in the back. The rest of it would just be retheming the inside and outside of the original buildings. Hopefully at least some of this comes true because that would really bring the park the face lift it deserves.