I would imagine that whatever operator ends up running this new HSR line would likely duplicate the type of service that VIA already offers on many of it's QC-W corridors. They have a certain number of "express trains" that do Ottawa-Toronto, Montreal-Toronto, Montreal-Ottawa directly, with no stops in between, and other trains that make the milk run stops.
If they run 10 trains a day (just a ballpark, and because the math is easier), what they could do is run 5 express trains, 5 local trains. Express trains would stop at: London, Kitchener, Pearson, Union. Local trains would stop at: London, Stratford, Kitchener, Guelph, Brampton, Pearson, Union.
The demand in those "local" cities would likely be significantly less than in the "express" cities, but I think that serving them with every 2nd trip or so would be worthwhile.
The other option too is incorporating the local service into what I've called (for the purpose of briefness, but also because it sounds good) SOGO (Southern Ontario GO). It would run current GO diesel stock to places like London, Brantford, Niagara Falls, Peterborough, and maybe as far as Kingston. The idea is that it would run local until it hits the end of or near the end of the GO REX lines (Aldershot, Mt. Pleasant, Oshawa), and then run semi-express to Union, stopping at only major transfer points.
This would end up creating a 3 layers of rail service: GO REX for the GTHA, SOGO for the area within 2hrs of the GTHA, and HSR for intercity trips greater than 2hrs away (by car). Nobody gets 'left out', but most people get the type of service that is most convenient for them.