The plot revolves around two regions at war, but in the distant past were the same. The issue could be the brotherhood, with the protagonists being siblings and separated by X reason. (politics, religion, armed conflict)

A version of the game could be South America (New World) and the other could be West Africa (Old World). At one point the game you would travel to the another region. Each region with 30 exclusive pokemon and 40 shared by both.

Seeing this in general, it would be something like retaking elements from Ruby/Sapphire and Gold/Silver.

I know GF never risk with something like this, but one can dream.