I think it would probably be better to turn the GO/YRT terminal into park space and replace a bunch of the parking with park space while we're at it.
The transfer between the subway and the GO/YRT terminal is far worse than the transfer to the existing TTC terminal, and also Hydro would no doubt fight against any sort of enclosed bus terminal under their wires, so it would be almost impossible to get a proper enclosed bus terminal where the current GO/YRT terminal is.
That said, the existing TTC bus terminal will probably be larger than needed after the subway is extended, given that most of the TTC routes using the terminal would no longer serve it. I imagine half of it could get demolished and redeveloped, or maybe a developer builds over the whole thing and builds a smaller bus terminal replacement inside, like CIBC Square or York Mills.