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I always thought they were really weak pokemon that couldn't survive in the wild so their race quickly started becoming extinct. And since the professors didn't want to see a species go extinct they took them out of the wild. And since they seemed so low-tier the professors give them to you, not really expecting you or the starters to accomplish much.
Then you train them to bomb-ass pokemon, everyone shits themselves and pays attention to you because you don't often see NPC's with fully evolved starters because they never expected much out of the pokemon in the first place.. I came up with this thought back when i was a small child, so my explanation is not without flaws..
