Here is my quick analysis of the 11 options:
Option 1: Too many transitions between above-ground and below-ground segments
Option 2: It will be very difficult to transition from below to above at the Stouffville Line as there is the hwy 401 and west highland creek
Option 3: Ok
Option 4: Too many transitions between above-ground and below-ground segments + weird connection with Eglinton East LRT
Option 5: It will be very difficult to transition from below to above at the Stouffville Line as there is the hwy 401 and west highland creek + weird connection with Eglinton East LRT
Option 6: weird connection with Eglinton East LRT
Option 7: Too many transitions between above-ground and below-ground segments + weird connection with Eglinton East LRT
Option 8: It will be very difficult to transition from below to above at the Stouffville Line as there is the hwy 401 and west highland creek + Too many transitions between above-ground and below-ground segments
Option 9: Too many transitions between above-ground and below-ground segments
Option 10: Ok, but probably very expensive
Option 11: Lack of direct connection along Sheppard Ave