Do we know for certain that Mewtwo isn't exactly that? Mew looks like some sort of cat, with big feet, tiny arms, and big eyes.
Mewtwo is WAY bigger than Mew, much more akin to the size of a large person. It also takes a bipedal stance similar to humans. It has developed longer arms with discernable joints, and now has fingers. It's skeletal structure also shares features similar to humans, such as the way the ribcage is positioned, how it's attached to the spine, and the way the spine supports it's head.
All we know about Mewtwo is that it was "engineered". Perhaps it's a bunch of pokemon DNA spliced together... but Mew already has DNA of all the other Pokemon. IMO, it makes more sense that they were trying to engineer some kind of Human/Pokemon Hybrid in a bid to acquire Pokemon powers for humans.
But... I just made all that up on the spot, and there's really nothing to support it aside from a few minor similarities, and that it makes a little sense.
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