My theory has always been that Mewtwo is just a mutated Mew, and Fuji's Mewtwo wasn't the first. A good real world comparison would be if humans were Mew and two humans had a baby with... hydrocephalus (big head full of fluid, it's a birth defect and very dangerous). Hydrocephalus Baby would be Mewtwo. Naturally occurring, but rare due to being a defect (then take into account Mew's own rarity and bam!) so what Fuji did was take the DNA of a healthy Mew and create a "defective" clone. Mewtwo.Alright, this one might be a bit of a reach, but something that crossed my mind watching the First Movie for Mewtwo's "birthday".
Does the anime at any point present absolute and irrefutable proof that the DNA Mewtwo is cloned from is Mew's DNA? Call me a conspiracy theorist, but I wonder if perhaps Mewtwo is based on not just an enhanced sample, but possibly a unique species of Pokemon like a mutation or deficient mutation/breed of Mew. To elaborate on my line of thinking:
- Mewtwo is supposed to not just be an exact, but an enhanced clone of Mew based on the DNA sample the scientists procured so that it can be the perfect fighting being. Yet if Mewtwo here is taken as accurate to the games, or we account for what a later portrayal implies, Mewtwo lacks a particularly useful battle trait: Mew's ridiculously expansive movepool. The manga's depiction gives a justification for this imperfection since Mewtwo was more of a hybrid between Mew's DNA and Blaine's, but in the anime the only thing ever definitively stated to be used in the cloning process is the supposed Mew sample the archaeologists found.
- The Team Plasma Mewtwo makes me wonder since a separate set of scientists ended up with what seems an identical Pokemon (Physically) despite having no reason for us to believe they had access to the work from the original; Mewtwo went into hiding and wiped the memories of Team Rocket, the only people who would both know of its existence and actually have notes of that sort regarding its origin and creation. If Mewtwo's DNA was that of a different species/genome, I could actually believe that they came to the same mon in what was more of a straight cloning experiment, rather than making the exact same enhancements to what are not-likely-identical samples of Mew DNA.
Even in the movie, I don't remember any empirical proof of the DNA's origin, as they recover the sample from a temple with something that at best looks like a few hairs, which I don't think would have enough DNA to reconstruct the important parts of an organism. Most times it's reaffirmed are Mewtwo boasting, and the best he can know is what the scientists told him before he obliterated the lab.
It would explain why Mewtwo has its own Mega Stones (which are supposed to be ancient, btw) because the specific gene that turns a Mew into a Mewtwo could've been accidentally recreated by Fuji as well as being what reacts to the Mega Stone, thus explaining the lack of Mega Mew (for now).