The French especially have built high-speed rail from the outskirts of cities to the outskirts of cities. They use a legacy network and have mixed traffic for the last mile going into the city stations. The same is true for all the other European countries, with the exception of Spain.
This is a very good decision, because it's so expensive to build additional tracks into city centres. I think this is really one of the advantages, and I've tried to address it from the beginning. This is also determining capacity constraints, because you have to share with mixed traffic, and you have to bring them into city centres to make the connections to the metro systems and the commuter rail systems to have a good interchange of passengers between your intercity service system and the local trains.
If you have smaller cities, and there are several examples from multiple countries in Europe, then you can really build stations at the outskirts, and there will be big park-and-ride systems, for example, to bring commuters via the high-speed rail system to the major metropolitan areas.
To make a long story short, go to the city centres of the most important cities—Toronto, Ottawa, Montreal, and Quebec—and build the stations outside of the smaller cities if possible. If you can't go easily through the cities, then you can't do it, but don't build any tunnels in the smaller cities. That makes no sense, the trade-off is too low to have the advantage of being in the city centre of smaller cities.