I think I have told this story before but - last time I was in Brussels I was taking a high speed train to France. I looked up the departure time and gave myself 25 minutes to be on the platform ahead of departure time - a very North American margin "just to be safe". I arrived at the station as planned, to find that five other trains were lined up to run through the same platform between my chosen arrival time and when my train departed. They all made their stops, departed, and yes my train departed on time. My point being - I am accepting that Alto could in theory be routed down the Stouffville route and onto the Kingston Sub with the right combination of higher standard of operating efficiency and high quality signalling. (I am more dubious that GO will run to that standard without a lot of dwell and padding.... right now 3 minute delays do not trigger bells, but the envisioned service would make those unacceptable)
The point is more - while that would be technically impressive, why needlessly put so many eggs in one basket?
The other missing factor is the potential for LSE to need to provide regional service along the Lakeshore. While VIA will probably be wound down, Ontario has good justification to seek an up to hourly local service at least to Kingston - Ottawa acknowledges the Kingston hub idea but is completely vague about what that will look like. The province may have to step up to enable this, but the need is there. So the corridor may house LSE express and local, Lakeshore Regional, Stouffville 2WAD, and Peterborough GO..... and then Alto. That's a lot of eggs!
I do think the Scarborough Jct needs the flyover, regardless of Alto or not Alto, because of those four or more routings that will have to be accommodated. Claiming that a flat junction will do is a pretty serious erosion of that location's operability.
And, as noted, even achieving 1968 times would likely make the Leaside routing a few minutes faster.
There are good arguments for both routings, and I suspect the Kennedy routing is being taken very seriously. I'm still of the view that it is a tradeoff that may come back to bite.
- Paul