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What are some of your favorite theories over the years that have ultimately proven to be untrue? Recent or retro, anything is fine so long as it's deboonked.
One I haven't seen mentioned much in recent years is one that I think was probably inspired by Monster Rancher, specifically that Pokemon were bio-engineered weapons created to fight in a war, presumably the one Lt. Surge fought in.
It's no surprise this one fell off, it was only really a viable theory for one or two generations. In gen 1, it was believable- Mew was the only "ancient progenitor" type Pokemon, and if you accepted his existence you could say all Pokemon were developed from him. Furthermore, real world animals still existed, lending credence to the idea these strange colorful beasts were a recent addition to the biosphere slowly replacing those that lack wacky abilities.
Of course, with Johto came Ho-Oh and Lugia, two more Pokemon with historical ties, and Unown, occupants of ancient ruins marked with their forms. Hoenn brought the Regis and the Super-Ancient Pokemon, plus more mundane relicmons like Claydol. And Sinnoh gave us the llama in an innertube said to have created all Pokemon, which was a nail in the coffin so final it probably wasn't even needed. But, as a tot at the height of Pokemania, it was fun to speculate.