Something that I was thinking about that would make a lot more sense was a different location for Museum Station. Currently, Museum Station is the last (or second last) stop of the University Line (before changing into Spadina) right before interchanging with Line 2 at St George Station. What I think should have been done, is to have Museum Station be an Avenue Station on Line 2, since there is a noticeable gap between Bay and St George Stations. The current "Museum Station" could also have been built, but rather it be called Charles Station.
Something amazing (at least I think so) that would be a result of an Museum (Avenue) Station of Line 2 is that there would then be the possibility of 4 interchange stations with Line 1: Spadina, St George, Museum, and Bloor-Yonge. Which could potentially spread out the load of people switching lines . It still doesn't completely reduce the Bloor-Yonge overcrowding, but still helps.
In addition to the different location of Museum Station, Queens Park Station makes no sense. There should really be a station north of the current station at Wellesley St, since that's actually in Queens Park (insert Downsview Park joke here). So the current "Queens Park Station" at College St could be called Hospital Station or something else that is not Queens Park.
Just one more thing I wanted to add, if you really wanted to be crazy for a fantasy "what if" scenario. What if instead of the University Line "ending" at St George Station, it went diagonally underneath the University of Toronto St George Campus from University & College to Spadina & Bloor. Then there can be one or two subway stations right in the heart of the University of Toronto, allowing for much better access. Then my previous ideas of better connections with Line 2 and the improved "Queens Park Station" would be irrelevant.
I just wanted to share these "ideas" I had, even if they never did or will happen.