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To be honest, the worst thing to happen to Pokemon as far as game design goes in my opinion was the transition from Gens 1 and 2 to Gen 3. Gen 1 was a game where you were just a person in a plausible world that happened to have interesting creatures in it. Gen 2 was a direct sequel that expanded the world, and added more "newly-discovered" monsters. Gen 3 was the start of shit like segmenting the Pokemon world into regions with regional Pokemon, regional villains, regional legendaries (that are basically gods now) with mystical-magical plotlines concerning the evil team that now gets rehashed every game, player character is the cliche "chosen one" archetype, etc. I realize that it's too late to go back now, but the first two gens (especially Gen 1) allowed the player to maintain more of a suspension of disbelief. I guess you could say the mystical magical stuff started in Gen 2 with Ho-oh and the legendary beasts, but that wasn't the main plot behind the game. That was more of an in-universe folk tale thrown in to give the world a sense of history. Maybe some people like the fantasy side of Pokemon, but I think Pokemon was special because kids could pretend like Pokemon might actually exist in our world hiding in the grass somewhere. I dunno. That's just my nostalgia talking.
