Only Game Freak can confirm it.
All it is is an incredibly famous theory, that is incredibly well supported with much detail, the only people that can confirm is Game Freak. Personally, I am torn as to if this is true or not.
But actually, it states here that GameInformer were interviewing Junichi Masuda and Takau Unno, two members of authority at Game Freak, and they were asked the question.
>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.
So yeah, they confirm it's not true. Hurrah.
Hope I helped. :)