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I think the evil gym leaders is also something that Special gets memed on for and I do get the criticism, but I also think it makes sense as a move to make the story more interesting and giving the villain plot more defined characters. There even seems to be a logic to the original selection process re: which ones are villains when compared to the actual Gen 1 gameplay, in that all the non-evil gym leaders are the ones who have Rocket shit going in or near their cities in their games, while the ones who are with Rocket don't, like they've already done all the shit they could do at home base or don't want their own town mixed up in it (with the exception of Saffron, which still makes sense because it's supposed to be a huge city).
So I don't have an issue with it overall even though maybe I am slightly salty it's all the leaders that actually seem to have personality in the games-- yeah it makes sense, but something like evil Erika could've been cool for example, since maybe you wouldn't expect it compared to the characters that already come off as brash/tough in the games. Especially with that weird /vp/ (?) theory that she's like a yakuza boss daughter type, like she and her gym are protected despite the Rocket presence in Celadon because they have mob connections or something.
The evil Lance/Elite Four stuff is where I think this aspect of Special starts getting too over the top probably.