I can only hope they'll have the sense to adjust the WiFi hack checks to start blocking Pokemon that have the pentagon, but at the same time have a memory of being transferred.
If not that, then they'd better at least check the memories of every Pokemon that's used in the actual VGCs, since until a sixth gen version of Pokegen comes out, it's an infallible method of determining whether a Pokemon is truly Kalos native or not.
Actually if you hack the Pentagon, it wouldn't have a memory of being transferred. Instead it says that it was hatched somewhere in Kalos.
http://puu.sh/5ZUIA.jpg ^ That's what it looks like if you hacked the Kalos Pentagon, then transferred it.
I'm talking about that girl who tells you your Pokemon's memories.
If the Pokemon is transferred, the first thing she'll say is "It has good memories it can't seem to recall", before mentioning a memory of its time in Kalos.
They could easily check for whether a Pokemon has the bit of coding that triggers that message and the Kalos pentagon at the same time, and block it if it does. As that bit of code is new to gen 6, there's no way you can fake it like you can the capture location.
Just a question.. if you have both copies of x and y, you banked 1 pokemon from x and transferred it to y.
Would it have the same memory as a fake "Kalos" pokemon? or will it be just like a transfer from a game to another?
If it is the former then they cant just block pokemon with "It has good memories it can't seem to recall" as it will also block many legit pokemons which people tranfer to themselves because they only have 1 3DS.
I guess we wont be able to find out until bank is released. Or if someone having the jap version of bank can help us check.