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Greninja is a purely manufactured-favorite. It got put in Smash, it got a more appealing design and better stats, ability, and movepool than the other two starters as well as being damn good overall, it got a super special part in the anime. It was chosen before ever being revealed to be the fan-favorite pokemon of its time. There was nothing organic about its popularity. And as soon as the fad was over, it hadn't been heard of since. That poll wreaks of meddling.
People being fans of Charizard caused Gamefreak and TPC to give it so much. Greninja was given it all before anyone had the chance to be a fan of it.
