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Introduce 'divergent' wild Pokemon.
All the begging for buffs to shitmons will finally come to an end, or at least slow down.
A divergent wild Pokemon has one greatly increased base stat. This stat is typically chosen at random but usually never includes the Pokemon's highest stat (unless Gamefreak wants to be a dick about some Pokemon getting a buff to their highest stat). So a divergent Blissey would be really fast, or divergent Sharpedo would have high defense. The lower the stat, the more it is boosted
Ecounters with them are rare-ish. Once encountered, a subtle flame effect plays and a message pops up "[Pokemon]'s battle spirit burns brightly!"
Gamefreak can also hide which stat is raised until the player catches it and sees for themselves. This mechanic will not only add more depth to breeding but also more depth and variety to wild encounters. Ideally you pair this with the right nature as well. Blows the meta open completely.