I always have thought the best option would be to turn the Stouffville line into "GO REX" with European-type EMU's (like the Talent 2
http://www.railpictures.net/images/d1/1/9/7/6197.1284931994.jpg) which is fairly "light" heavy-rail, so perhaps community opposition would be minimal as long as you convinced them it wasn't a huge noisy GO Bi-Level. You would need an exception from the FRA rules, but GO was investigating doing this as long as the trains stopped at Kennedy. (You wouldnt get an exception to Union, simply too much rail traffic)
Then, add a fork at the SRT at Ellesmere and have every other train run along the SRT. I am sure a rebuilt or reinforced and modified elevated tramway would be needed, but then you would have one line that services the whole scarborough area. (You could scrap the subway plan too)
Interesting idea having it continue along to Pickering Airport.
Perhaps it could be built along the ravine thats in that area, with a stop at Centennial College and then up to Malvern Town Center and continue along the CP corridor.
All speculation, I know nothing about the area.
One line to rule them all!