1. Mewtwo is only a "clone" in the anime. In the games, Mew gave birth, and scientists (Not Team Rocket) altered the baby's DNA to become Mewtwo. Notice how "Mewtwo" sounds like "mutant?" It's a genetic experiment, not a clone. Mewtwo is Mew's offspring that was genetically altered.
2. Ditto is not a failed Mew clone. Masuda himself debunked this.
3. Genesect was originally an ancient insect Pokemon. Team Plasmsa revived it, then gave it a laser cannon.
I don't see why being created by science makes it impossible for Mewtwo to have a Mega Evo. Since Mewtwo is actually a Mew that was altered, Mega Mewtwo is what Mega Mew would be if it was altered.
"The difference between fiction and reality is that fiction has to make sense." -Tom Clancy
"real pokemon" is an oxymoron. you could say "true pokemon" but there is no such thing. every 3 years or so, new pokemon are released. if someone came up with the exact idea of honedge a year ago, would you say it wasnt a true pokemon? also, mewtu is made from mews genes. so it is definitely a true pokemon. not all the pokemon pop up out of nowhere, theres evolution (in a darwinistic sense) in the pokemon world probably, too. Is a chicken a true animal because it was bred from feasants and similar birds?
Xerneas, the gay-pride Pokemon 3DS FC: 4511-0558-9256