Okay ... being realistic here;
Get rid of Gibson Amphitheatre and create Spiderman/MIB attractions.
Gut the Monsters walk through and the building behind it (I believe that is just the big building they use when it's raining and for other events) and make a Universal Monsters omnimover attraction with AA's, etc. Would be a GREAT fit for the park.
New film for Terminator, could even be something to do with Avatar, doesn't necessarily have to be Terminator.
Updated Shrek film. I love the franchise but it's just after the 1st movie. With the fourth and (reportedly) final movie coming out would be a good time. OR ... replace it with the Jimmy Neutron/Nick attraction from FL. That thing is awesome.
Bring back wild west stunt show.
New show to replace Waterworld. Great show, but it's time for something new.
As was mentioned by CoasterMatt, replacing the Animal Actors/Creature theatre with anything significant isn't possible due to the hill.
As much as I hated Transformers 2, that will hopefully be good for that area.
Expand Mummy building (up) and re-do the coaster part of the attraction to make it more like FL's Mummy.
Not sure what more (if anything) can be done down there without using more "Studio" space.
For God sakes, get rid of Fast and Furious and War of the Worlds.
Agree with the updates for Jaws.
Keep Earthquake, but maybe some updates would be nice?
Update spinning tunnel, don't need Mummy there still. Bring it back as a snow tunnel or updated Battlestar Galactica.