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I think the biggest problem from the start was GF allowing people to transfer their Pokémon over to other games or store them in a cloud.
If Pokémon were not made transferable between different generations from the start, then none of this would have happened. GF would have simply had to animate and model (Yes, I know they future-proofed since XY) the Pokémon in their respective games and that's it, people wouldn't have become so attached to their Pokémon and people would have learned to let go, much like Digimon fans.
The other thing that's wrong with Pokémon in addition to transferable Pokémon is IVs. People became too obsessed with getting perfect Pokémon which made them even more attached, immensely more so if they got a shiny. If Pokémon had pre-obtained EVs instead, the only thing people would have to work for is getting them to 0 and then train them to their desired stats instead.
Ultimately, they doomed themselves from the start.
GF is indeed very lazy and incompetent, especially when you look at their code and know how bad their games are from a technical standpoint. But if they didn't have to deal with so many and ever increasing amounts of Pokémon to put in every game, maybe they could have put more effort in other things from the start and improved more than they do now.
