I think we're all forgetting that Mewtwo blew the lab up when he woke up in his tube. Therefore he recreated the machines for his own use. While they were still cloning machines, Mewtwo's intelligence probably helped him redesign the machines to make them better. Or more likely, the cloning machine works perfectly anyway (consider the cloning of fossil pokémon), and the reason Mewtwo is so different is that he was extensively genetically modified (as Giovanni requested).
I kinda like the idea that the cloned Venusaur, Charizard and Blastoise were prototypes of shiny pokémon. They all had markings all over them, but maybe that was just so they could be more easily distinguished in the early battles. In the royal rumble towards the end we didn't really care which was the original and which was the clone; we only cared that they were fighting to the death. It wasn't as important to distinguish between them, so the creators could just be lazy and copy-paste the pokémon (so to speak). Also, they were the first clone pokémon we saw (besides Mewtwo himself, who doesn't really count since he's a new species rather than a direct clone), so there had to be something sinister about them, and evil battle scar-like markings manage that.
Also, Mewtwo created the cloning machine such that it directly cloned the pokémon. When Giovanni commissioned Mewtwo to be created, he wanted an uberly-upgraded version of Mew, so Mewtwo's genetics were messed around with so much to increase his psychic potential that he really did become a different pokémon.