How about this:
What if the main games didn't have all the pokemon going forwards but the content they're teasing in Home was like an official showdown? You'd still have to play the main games to catch and raise pokemon, but you could transfer over and use whatever you wanted for online battles in Home.

I know, given what GF has shown they're capable, it's a long shot and a half (if it's classic sprites maybe they could manage?), but IF that's what happened, would you consider that a reasonable compromise?