>>58207232
Instead of 2 games, do 1 game and let's say you have 10 'exclusive' Pokemons so 2x10.
Give a random number in base 2 or give one from an algorithm from the player name, like in Dragon Quest or any other way. It's best if the player can't decide the number.
Zone 1: if the first digit is 0, the first exclusive will be Pokemon A, if it's 1, it's Pokemon B
Zone 2: same but with the second digit
For legendaries, either use the same system or better, let the player choose between two paths during the story so they don't choose according to the game cover but from their point of view while playing the game which is more engaging.
With a 10 digit numbers, it's 1024 versions, with 20, it's more than a million. You only need one game and can still try to exchange the Pokemon you cannot have with your friends. Perhaps one of them doesn't have it either, ok let's find a third person who can exchange it with us. Moreover, each new game will provide the feeling of surprise because you wouldn't know in advance what will be your Pokemons.
Game Freaks will not do it because of greed but for me, it would be the perfect choice to keep things the way they are without needing 2 physical versions and adding a little bit of surprise.