It won't be that way, only the "legit" generated Pokemon will make it through. It's already been announced that Pokebank will be able to confirm if the Pokemon is hacked or not, similar to the online mode in B/W.
Oh, the Masuda method. I would recommend Ditto, but trust me, the moment I see a foreign one up in the GTS, it keeps saying "This Pokemon has already been traded". Just about everybody is keeping an eye out for them. I did eventually get a shiny+Masuda one, but it costed me my Xerneas. The reason I bothered trading it is simply because of this: I don't use any Pokemon in the Uber tier for battling, I always participate in OU matches. Therefore, having Pokemon with great stats all around mean more to me than legends.
It would be easier actually if you did get one from the wild to pass down the right nature. The Ditto's would then be used to pass down the desired Iv's. Might be hard, but if you're lucky, you might just be able to catch a female with the desired nature(of course meaning egg moves). I honestly just managed to catch an Adamant female Scyther (Iron Maiden ^^) with Technician today by luck.