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It's almost as if Gen 2 were designed as direct sequels rather than standalone games, and in order to remain consistent, the new Pokemon had to be recent discoveries tucked away in corners you weren't allowed to explore, featured elements you didn't have access to in Gen 1, or were extremely rare to explain why they weren't found in your romp in RBY, especially considering you can't hand-wave it with "oh, they were HERE this whole time" because Johto is literally conjoined to Kanto to a point where they share the same League.