Well if the feds ever end up implementing high-speed rail out that way, there will need to be a serious look taken at the whole area. A west-GTA station is needed, and so are grade separations and additional trackage.
Here's my suggestion: a new station right at Bayview Junction.
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This will allow all trains (Oakville to Dundas sub, Oakville to Grimsby Sub, Dundas to Grimsby sub and all vice-versas) to stop here, and then continue without backing up. It would also make connectiosn convenient for passengers.
Here's a scenario: a passenger from London gets on a VIA (HSR) train, and wants to go to Niagara Falls. They get on a train heading to Toronto Union. They get off at Bayview, and transfer to a different VIA (or Amtrak) train heading from Union to Niagara Falls. Operations are simplified and given lots of flexibility.
Also, it would be a connection opportunity with a rapid transit line identified by Hamilton Street Railway (the 'L line') that will go between Waterdown and downtown Hamilton.
The three challenges with this:
* Cost: It would take a hell of a lot of money to ensure adequate car connections between Highway 403, and that a sufficient sized car garage and other station facilities are squeezed onto the site (or built upon adjacent sites). On top of this, the grade separations to ensure that there are no conflicts between trains (passenger/passenger or passenger/freight), and adequate bike and pedestrian access.
* Technical Requirements: Squeezing a 12-car GO train in here? Might need some track shifts...
* Environmental Impact: The station would need to ensure that all potential impacts to the surrounding Cootes Paradise are mitigated.