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There's tons of ways you could implement individuality for pokemon that don't obligatorily make most pokemon shit and force a tedious eugenics simulator to get the best potential out of a pokemon. Small physical features, size differences, coloration differences, randomized characteristics, working in a nintendogs-esque system of name recognition and learning through pokemon-amie, etc.
And that's not counting the ways that pokemon are already individualized, such as nicknames, the conditions they were captured in, their natures, their abilities, their moves, their EVs, and the player's own experience with the pokemon.
GF is just too lazy to rework a system that doesn't affect the majority of their playerbase. It's simply not worth their time and money to alter the formula that's kept them running for such a small faction of their customers, and that's the cold reality of it. We just get to sit here and deal with it.
