Is Ditto a Failed Mew Clone?
According to an GameInformer interview with the art director and the producer (Junichi Masuda) from Gamefreak:

There is a rumor that in the original Pokémon games, versions Red and Blue, that the Pokémon Ditto was a failed attempt at cloning a Mew. I was wondering if you could speak to this, to whether or not it’s true.
Masuda: That’s the first time I have ever hear that rumor actually.
Is that your only answer?
Masuda: In terms of how Pokémon are designed, they are each their own unique living being. The unique thing about Ditto is that it’s a Pokémon that can change forms, but each Pokémon we create with its own unique element, so we just make sure that they are all individual life forms of their own.

Though it seems that his response denies this theory (or rather skirts around it), but since he was probably not directly involved in the development of the game, it's still possible that Ditto was originally meant to be a failed Mew, but scraped somewhere during in the development cycle.