The recent (February) Metrolinx report on the various GO stations actually predicted ridership to decrease on the Richmond Hill line ... (2040s?). I suspect from some other numbers, that there's a weakness in the modelling for remote and infrequent service - but a service increase seems very unlikely - at least south of 407.
If the service really is frequent, then one could have more than one suburban station, with different trains stopping at different stations. As they'll be a stone's throw from Sheppard East station, where Line 2 and Line 4 (and maybe even Line 7) will intersect, that seems like a decent spot. Maybe 407 as well.
Which would be tough topographically. I'd put my money at Don Mills Road, with a new Ontario Line station.- though it's a bit close to Science Centre station, and would require a lot of redevelopment around there. Another option is that if they put a new Line 4 station half-way between Midland and Brimley - which might make more sense than trying to sick a station at either road, and simply have one station between Kennedy/Agincourt and Sheppard East (McCowan). But we are approaching fantasy land.
I don't see a fly-over (or under) as a show stopper. If GO can build them, so can VIA. If they use Stouffville, they are also going to have to cross the CP tracks somehow, or have a massive or very tight curve on the north side, given the geometry up there; not to mention the issues at Scarborough Junction, and the loss of the easy ability to add a 5th track between the Don and Pape with the Ontario Line taking the last two possible tracks.