I would run a true high speed Windsor<=>Chatham<=>Kitchener<=>Pearson<=>Toronto<=>North Pickering<=>Peterborough<=>Kingston<=>Ottawa<=>Mirabel<=>Montreal<=>TroisRivieres<=>Quebec City.
With hubs in London, Toronto, Kingston, and Montreal there would be regional services on the existing rail corridors rather than the high speed one.
London Hub (VIA SWO): Windsor, Sarnia, Kitchener, and Toronto via Aldershot.
Toronto Hub (GO Transit): Niagara/Hamilton, Cambridge, Orangeville, Kitchener, Alliston, Barrie, Sutton West, Uxbridge, North Pickering, Bowmanville.
Toronto Hub (ON): Sault Ste Marie via North Bay, Cochrane.
Kingston Hub (VIA EO): Toronto, Ottawa, Montreal.
Montreal Hub (AMT): Rigaud, Candiac, Saint-Hyacinthe, Mascouche, Saint-Jerome, Mirabel via Deux-Montagnes.
Montreal Hub (VIA M): Sherbrooke via Saint-Jean-sur-Richelieu, Quebec City via Drummondville, Ottawa.