The only game to do this was R/S/E, and I feel the idea was really cool. Two very strong Pokémon, with one being unlocked after defeating the champion. I genuinely feel they could have explored this further, like a version-exclusive pseudo-legendary, where you unlocked the other after beating the champion.
They could have one as the main Pokémon of the villainous team leader and the other as the champion's. Or even a pseudo-legendary that could evolve into two different forms depending on the time of day/night.
by InuMatte