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I unironically am loving Lets Go Pikachu at the moment but I do think this shit is fucking stupid. Either make it it's own game or play it true to the originals, this is just weird
What it feels like is that they made the Red/Green/Blue models with the intention of them being the MCs, but had to change them later down the road, possibly because of features like customization or possibly just because Masuda's going senile and mentally ill. The devs didn't want the models of the original MCs to go to waste so they pulled this weird alternate timeline post-game bullshit out of their ass so they had something to use the models for
I obviously have no proof of any of this but it's the only explanation that makes any kind of reasonable sense in my mind, even by modern Game Freak's standards