Really like Reece's ideas, and I've had many of the same thoughts. One of the things I'd like to see incorporated into a future Pearson Central is a dedicated platform for cross-border Amtrak trains.
The idea would be that Amtrak trains to New York and Chicago would start their journey at Pearson instead of at Union (with such good transit connections from Union to Pearson in this scenario, it's not like it would be tough to get there). Passengers would go through a US border pre-clearance area like at the airport itself, and then would be directed to a separate waiting area and ultimately a segregated platform. Pearson has the unique ability to leverage the US pre-clearance staff already working at the airport, so staffing shouldn't be an issue. From there, Amtrak trains would operate non-stop to Detroit and Niagara Falls NY, and would effectively be sealed until they crossed the border.
The path to Chicago would be pretty obvious, but the path to New York would involve using the Kitchener corridor and then transferring onto the CN Halton Sub, and connecting to the Lakeshore West line just west of Burlington Station.
One of the services that would need to go hand-in-hand with this would be two "International Shuttles" that would basically be DMUs that would run between Windsor and Detroit, and Niagara Falls ON and Niagara Falls NY. You would board at each station like any regular station, but upon reaching the other side you would immediately be directed to a Customs booth. Once you passed through that, you would be able to access any connecting services at any of those stations (Via, Amtrak, GO, etc). I could see those services becoming popular options to cross the border even without the enhanced Amtrak service.
For Amtrak though, what this shuttle service would allow is for passengers coming from or going to points in between Pearson and the border is for them to take either Via to Windsor or GO to Niagara Falls ON, then take the international shuttle to cross the border, then catch the Amtrak train coming from Canada on the US side, and board it as a domestic train. All of this would have the net effect of eliminating the border delay with trans-border trips. For the return trip, passengers would clear Canadian customs at Pearson just like they do now when arriving on an international flight.
In short, building a brand new train terminal from scratch is an excellent opportunity to build a proper international rail facility, leveraging existing staffing and border inspection logistics. If the US is going to get serious about building HSR or even Higher Speed Rail, we need to make sure we have the appropriate infrastructure to connect into that network, and to make international travel as seamless as possible.