Again, the LRT system itself was flawed. They do not allow for seamless transfers between the existing system, or the bus network, which, in my eyes, makes them extremely flawed. The reason the grade separated option wins is because of the transferability between other routes. Eglinton East works because it serves the corridor it travels on, not to be fed by other bus routes, and it connects directly with the Eglinton Crosstown. The SRT replacement LRT wins on transferability between buses, but not to existing transit, and, capacity is decreased, while dwell times increase. The beast solution for that corridor without a subway is to replace the SRT with ICTS, it's even cheaper than the SRT replacement with LRT. The Subway wins because of a seamless transfer at Kennedy, and the fact that you (should) easily be able to transfer from a bus terminal to the subway. The Sheppard East LRT loses on all accounts because it's just a capacity increase of the 85 bus, which, quite frankly, isn't the best bus to replace with LRT right now. I can think of at least 10 other routes that would be better suited for LRT than the 85.
Also, more stops does not equate to better service. Redundant stops only increase trip time and reduce the willingness of people to take transit. I'd much rather bike to a subway station or take a bus to a seamless transfer at a subway station (even if it ends up taking 5 minutes longer) than taking a bus or walking a long way to the LRT stop. Why? It's far less stressful, and it means there's storage for my bike if that's my choice off transit. Scarborough is, generally, not dense enough for LRT, but it is dense enough for 1 or 2 dedicated transit priority corridors that everywhere else feeds into. With the LRT plan, not much is changed.