You can use an English version of X/Y with PokeBank on your JP 3DS.
Pokebank accepts them, you just can't play the games themselves.
Which is pretty dumb...
I'm saying the region lock might not let you play the English Pokemon game on the Japanese 3DS as was suggested. *Edit* to word what I'm saying better, the Japanese 3DS might not even recognize what was put into it as a game and give it as an option to transfer, kind of like when you put a super famicom cart into a super nintendo it wouldn't do anything.