I don't like the loop idea of connecting Sheppard to B-D. I don't think many would go all the way around. I would rather see B-D extended north to Finch. I understand that space was available in the CPR rail yard, so have a subway train yard there - and possibly a Finch station on the north end of this yard. You could likely sell the Greenwood yard for development to help pay for this.
It all goes to what alignment that McCowan Station should be at.
For Sheppard, which I agree could be done after, I like the original plan of it going to Agincourt GO, then heading to STC. As an extension, it could then go to Centennial and UTSC. The question then becomes, should the shell be built now for the STC station on the Sheppard line.