>>44588528They could do something along the lines of each version having the player explore a different region, then being able to "link" with the other version to explore it in post-game, a-la Oracle of Ages and Oracle of Seasons. I've heard they wanted to try something like that for Black & White but didn't, for one reason or another.
Two regions, one based on Chugoku and the other on Shikoku, would be great for this. One being more calm and rural with strong Buddhism-influence, and the other more busy and urban with sprawling buildings and technology.