Just for clarafication, is the OP's plan to create a massive collection of Mewtwos with values for attacks that are currently unoccupied, transfer all of them, and then see which previously unoccupied values suddenly turn into new/undiscovered moves in X and Y?
I am endeavoring to make progress on IR's work with his Python-based GTS manipulator, and with his permission I've uploaded an updated version
I am endeavoring to make progress on IR's work with his Python-based GTS manipulator, and with his permission I've uploaded an updated version here: https://code.google.com/p/ir-gts-new/'>here . Unfortunately, he was not responsible for the majority of the crucial back-end work, someone else by the name of LordLandon wrote the code that essentially spoofed the GTS server. It may be worth checking up on him and whether he's interested in trying to figure his way around X and Y's GTS.
I, too, tried sifting through packets that were sent to and from my 3DS during a GTS trade, but Nintendo has not been stingy with encryption.