I think part of the reason why the layout is such a dog's breakfast is because Ryerson didn't let them implode the parking lot. If they didn't have to build around it, then the layout could have made much more sense. As it is, the loading dock has to go all the way to the back wall of the lobby. If the parking was moved underground, the loading dock could've also been moved, and the retail element could have extended all the way up Victoria like a galleria. Similarly the HMV building could have been incorporated.
I don't think there's any real fixing the building without demolishing it. I imagine someone will come along in 10-15 years and rip the whole block down and stick a few towers on the site, atop a podium that does a better job of doing food/entertainment/learning/office better than the current state. Even if you ripped down the Ryerson lot, you've still got the elevator cores and stairwells in the way, and forget about moving those. The building needs another passenger elevator for the lower floors because it mysteriously only has one.
I remember reading a long time ago that the pillars for the building were designed to handle a roller coaster that never was. Perhaps that's why the office layout on the top floors doesn't extend deep into the lot?