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Even if they did come from Mew, it could explain how Ditto became so much more numerous. A few Mew some how evolved (devolved?) into Ditto, which then propagated itself through mitosis or whatever, or a few failed Mew clones got out of their laboratory and did the same.

Maybe they can divide like amoebas when nobody's looking.

Honestly the only thing I'd change about Ditto in-game would be its inability to breed with itself, just to make my shiny hunting a bit easier.