In addition to the Pixar retheming of the HISTK area (which I like, so I'm not saying I want them to do that), they could redo LMA to make it Cars related...and hopefully entertaining, something it isn't now. Additionally, they could kill that pathetic Narnia walkthrough and perhaps put the Crush coaster or Pizza Planet there.
As much as it pains me to say this, the Tour probably should go, too, if it's going to stay in its present state. They could do something like Universal, though, and keep Catastrophe Canyon as an attraction unto itself, and perhaps turn the area the tram used to drive through the Costume Shop as a walkthrough. These are pretty much the only highlights of the tram tour left anyway, except the Boneyard, which could be its own area, too. People might enjoy being able to have their pictures taken next to some of those vehicles and props. Then maybe they'd also keep them in better shape.
After the Tram Tour is gone, then the unused areas would all be free for developing. They could even slap in a clone of DCA's A Bug's Land, adding more kid-friendly fare to the Park, as well as a relatively cheap way to get 4 new attractions (I'd love to see an expanded Heimlich's Chew-Chew Train).
And for gosh sakes, do something with the Hunchback Theater. They could use some of that Tram Tour space to build a place to store the Osborne Lights (maybe make it walkthrough, too...another relatively cheap attraction), then put a new show in the Theater itself.
They could really get a ton of "new" attractions out of this thing, if done right.