I never pre-order games period. If you pre-order games months in advance these stores make interest off the pre-order money.
I buy a game on the first day, there are always plenty of games in stores on launch day. I am not interested in Limited Edition games so no need to pre-order.
48 hour limit for pre-order pick ups is a crap policy they should give you a week minimum. I would not return to the store if I was in your shoes.