I liked the idea of the City Hall station on the Relief Line. Even better would be to double track the Queen section of the line to route some GO trains there, combining the Relief Line with that proposal for a GO Lakeshore Queen tunnel.
In my opinion having any kind of tunnel for the GO RER system is a waste of money and a poorer option than the Bathurst North Yard idea.
http://www.metrolinx.com/en/regionalplanning/projectevaluation/studies/studies.aspx
Many transit systems, like Montreals AMT and Chicagos METRA have two stations downtown connected by a subway line.
Some trains serve one station and others serve another.
I also think that Toronto North station should be reopened, and every 3rd train or so from Milton, Kitchener, Barrie line service this station, once we get less than 10 minute frequencies of course. Then of course eventually Seaton/Peterborough GO lines in the future.
https://en.wikipedia.org/wiki/North_Toronto_railway_station
All of this relies on the Relief Line however: to link Bathurst North station to Union, and to not cause overcrowding on the Yonge line when Toronto North station offloads people who will take the line at Summerhill station.
We already need the DRL, and so to me, creating a spread out web of 3 stations, Bathurst North, North Toronto, and Union station, will much better disperse commuters throughout downtown Toronto rather than building an expensive tunnel under Union and cramming more people into that god awful busy place.
Perhaps another layout would be that the Express Diesel trains from particular services go to Toronto North and Bathurst North and all the inner city RER trains go to Union. Perhaps people from out of town would not be concerned with getting to Union or vice versa.