Basically, our format had been Pokemon XY version, but they're essentially the same game with minor differences. Now, what if we had two closely related regions (think Kanto and Johto), both games have one region of each. It basically justifies why there are version exclusives, because they are in different regions.
The plot would be different for each, but you get to play a linked game where you either continue X-->Y or Y--X. No order is specified, and you get to see even more differences in the story based on what you link to what.
The way I see it, it would actually justify buying both versions, and possibly even the same version a second time so that you can restart one, allowing you to do a X-->Y1 (restart X) Y2-->X, except the story differences is almost justifiable