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The obvious answer is that Pokemon are aliens that replaced nearly all animal life in earth with themselves. That's why so many of them look like living creatures.
"Bbbbbutbut the inanimate object ones"
Occasionally Arceus made mistakes and assumed these objects were living companions to humans, and thus tried creating creatures to replace them.
"Butbbuubtt fossil pokimens"
Previous Pokemon assimilation attempts probably detailed the ecosystem enough to cause mass extinctions.
