After thinking about it, I hereby decree I'm not a complete jerk but also not a complete good person.
For the person I inconvenienced, yeah, sucks to be them but they will get their Deluxe set the next time Gamestop gets a shipment. I see it as the same kind of inconvenience when someone rear ends you and you have to deal with the insurance. Sucks for them but they'll be made whole by the person who inconvenienced them-- Gamestop.
I don't really feel bad about taking of the clerks stupidity, in fact, I don't even know how they'll trace it to that specific transaction so he'll probably get off without anything. In the end, it will probably be the manager that gets in hot water and the manager probably deserves it for hiring people that can't tell the difference between the two bundles.
-edit-
And I haven't really had a chance to mess with it much yet besides just getting everything set up. The only thing I can say about it so far is that switching back to the main menu is incredibly slow (like 20-30 seconds).
