Turns out, being evil doesn't change your Pokémon's colors, but being a main character does. Fight the aeons! Control the dark aeons!
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Yuna's aeons have the dark skins; possessed aeons have the normal skins; the dark aeon superbosses have the normal skins.
The original mod had some flaws. I also had some issues with actually getting a couple dark aeons to inherit new textures, not sure if that's the mod being flawed or me. In any case, I've made sure the files included in this repost will work on all the dark aeon superbosses, the aeons possessed by Yu Yevon, and all of Yuna's aeons.
Please gimme a comment if you find any issues. Here are the problems I know of:
Yuna's Dark Yojimbo's face has the normal version's colors. Likely needs manual editing. Fixed in V1.2
Belgemine's Dark Yojimbo's face has the same issue above.
Belgemine's Dark Anima's lower half has the normal textures. I can't get the texture ID for some reason. If you have it, please share—
Unlike Nikon, I did not sort all these files. If you want a specific character changed, good luck. Enjoy!