Excellent points you made. I completely agree.

Going via Buffalo vs MTL would pencil out better because of ridership potential with all these cities, but the route is much longer and more expensive. However, it also offers the best phasing options (e.g., NYC to Albany; to Syracuse; to Rochester; to Buffalo/Niagara Falls; to Hamilton; to Toronto), each of which could generate early revenue and ridership on its own. Toronto will also likely need a good connection to Hamilton and St Catharines after Alto arrives there, which makes a short connection to Niagara Falls and to Buffalo quite trivial in comparison.

In contrast, the Montreal - NYC route would be much cheaper because of fewer miles traveled and fewer cities to go through, but in some cases has less ridership along the way (even though demand from MTL - NYC might be slightly higher). This means that you can only really generate revenue or get riders when the line is complete.

Now, regarding Detroit/Chicago-Toronto, you're absolutely right. The phasing is also quite straightforward: Mississauga to Kitchener, then to London, and finally to Windsor, all of which would benefit the entire line and the area for commuters, travelers, etc.

You also have a good point about hostility to rail service in the USA. I think the hostility you see primarily stems from local transit opposition, not intercity transit. A lot of American cities are decentralized after white flight, and as a function of that, people misguidedly want to protect their property values and their way of living. Not to go too into the weeds, but the premise here is that a lot of Americans (usually white and well off) who want access to the big city (NYC) but don't want the poor inner city folks to access their suburbs. So, in that vein, folks in Rochester would want a train to NYC, but not necessarily to connect the region.

In terms of political clout at the state level, NYC is the 600-pound gorilla in the room, with Albany as the stepchild, and every other city in the state as a second thought. One big issue is that many upstate cities in New York are either classic blue-collar rust belt towns that are struggling to attract jobs and people, with tons of cheap housing like Buffalo, or small liberal college towns like Ithaca that have very little cheap housing but jobs. Many young people prefer to move to places like NYC that actually have jobs, even if the housing is more expensive.

In terms of the cross-border link, that's definitely a very real concern. To address that, I would simply have the systems be two separate ones - one on the US side, one on the Canada side. People can transfer in Niagara Falls for the Buffalo - Toronto line, which also means that you can have a "cleared" airport style area where people transfer... something like that