As long as the network is constructed properly you can offer any combination of services you desire. Any stations that are directly on the high speed line would have two additional tracks so trains not stopping at the station can bypass should another train be waiting there. A lot of towns could have short spur lines off the high speed line, probably 10km in length or so so that it could provide good access and again offer a chance to let express trains jump past them. I could easily see direct Toronto-Montreal service with only stops at Pearson and Dorval, if that, working well for business travellers in morning and evening hours. You could also have milk runs that make all stops, basically two train sets could make two round trip runs each day making all the stops, and since it would utilize the high speed line along much of the way, these trips would probably be equivalent, maybe even a bit faster, than what an express trip takes now. And you can have all combinations in between that would see places like Kingston getting a large number of stops, probably places such as Port Hope/Cobourg or Brockville getting a few extra stops on top of the milk run, or whatever works out best in the end.
And it isnt hard to lure people into using slow trains. Just charge by total trip time instead of distance. Express trains cost the most, milk runs the least. There are plenty of people who would add some time to their trip to save some money, such as students, or seniors, or people who don't really need to get from A to B as absolutely fast as possible.
Edit: I also agree with unimaginative that the amount of revenue that could come from Kitchener-Waterloo in particular could be much more than most would suspect. Again, it is a matter of building into the network the ability to serve these sorts of markets, but without making it necessary to always stop there.
Edit: And don't forget that most reports expected ridership to go from 4 million to about 11-12 million in a 10-15 year period. So if now you have a stop, such as Kingston, which on average fills 1/2 to 3/4 of a coach, then with increased ridership each stop could end up filling 1 1/2 - 2 coaches which is a significant number of passengers. Same is true of all the smaller towns. They may not have much ridership now, but, if you operate milk runs that can utilize a lot of the high speed line and reduce time quite significantly, these ridership numbers are likely to rise quite a bit too.