Keep in mind a region's scientists may actually have limited knowledge of science and medicine, than another country, especially one that is obviously going to be tight lipped about genetic breakthroughs (think of the show called Eureka).
The Kalos region is heavily DNA themed, or so we're guessing, which mean these scientists were born and bred to know about genetics, and most likely cloning.
Kanto on the other hand, has sciences in other places, Kanto created the master ball, and some other things, and we're not focused on genetics.
But I do agree, that the creation of another Mewtwo, with NO plausible explanation is bad writing pure and simple. ESPECIALLY since it's called Mewtwo and isn't green.