I would:
a) Change up the queues of the USF attractions and remove the TV screens and fake cameras except the ones that are in Production Central. They shouldn't really feel like you're in a movie set, for example in the Mummy the queue shouldn't have cameras it should immerse you into an Egyptian Museum.
b) Add a Grinch family coaster to IoA
c) Add a Rocky and Bullwinkle dark-ride
d) Fix the outdoor portion of the Spiderman queue, it's horrendous.
e) Improve KidZone, and re-name KidZone. Take out Fievel, Curious George, Barney, and Animal Actors. Refurbish ET Adventure, add a Spongebob boating school ride like the Speedway, and move Shrek 3D
f) Give a mini-land dedicated to Universal's classic movie monsters replacing Fear Factor Live. With Monsters Café relocated, a ride through classic horror movies, and House of Horrors
a) Mummy takes place on the film set, that's the story. "The Curse! It's real! This whole place is a trap!" Unless you are planning on changing the whole story...
b) There are already rumors about a Mr. Crumpet roller coaster, but they have somewhat been shoved aside since....
c) There is the possibility of a Lorax themed ride, since the movie did very well. So if there's a new dark ride, it'll probably be that.
d) Kidzone expansion is obviously necessary so good idea there. Moving shrek is pointless, but the rest needs to go. Definitely refurbish ET, Expand Spongebob presence, but focus on Dreamworks and Universal animated movies for this area.
f) As much as I would love a new area with the Universal Monsters, you can't get rid of the Fear Factor stadium for one reason: Bill and Ted.
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Honestly, Once one more ride opens in Islands (Mt. Crumpet, JP Ride, Lorax, Or whatever it may be) and the current USF expansions are done (Tranformers, Diagon Ally, Simpsons, ETC) I would focus on the experiencial issues.
The food service at both parks need complete overhauls, especially the quick service. Live Entertainment needs work too, Animal Actors, Beetlejuice, Sindbad, all of that needs to be re-imagined.