May I inquire where you purchase your tinfoil hats? There was a black van parked 3 blocks from the place I used to buy mine from, obviously I can't go back there anymore.
Just to keep things in perspective, 6 months ago it wasn't too hard to find a copy of Xenoblade. There weren't multiple copies in every store, but if you looked around a bit you could find a few in your city. That's when Gamestop started hammering on trading the game in. Then the proverbial well began to run dry. Gamestop began hording them in preparation for this promotion. As for the different cases, it's entirely possible that some time during the print run the decision was made to change the case. Games, like most things, are printed in batches, and certain details can change between one printing and the next.
Metroid Trilogy should be proof of this. Why would Gamestop go through the effort of recreating the Xenoblade packaging, right down to the Club Nintendo insert, and not create a case and box art for Metroid? Do you really think that they'd go through the extraordinary effort to set up things to reprint the game and then figure it's too much work to create something to put on the cover? And do you really think that a reprint would happen without there being some kind of solid confirmation, not just a company responding to baseless accusations from a very small community?