A) just because your unit cost you $499 (as if that's anything new) doesn't mean that you're entitled to a brand new unit. They're within their rights to actually give you a refurb and give it time, those returning for "issues" will soon be handed a refurbs just like the iPhones.
B) Thoughts are that I too was surprised when my exchange resulted in a brown box. They took the new one out of the brown box and put it in my white box. My box doesn't match the serial number on the iPad but that should never be an issue, I have all of the paperwork associated with the exchange anyway. I did ask Apple (both retail and over the phone) and was met with the same response, it's new and not a refurbs but they're meant to be used as in-store exchanges until the refurbs start coming in. In other words, be happy you did get a brand new one.
Did you not leave with a $499 brand new iPad in a white box or did you get a brown box, they're supposed to have you keep the white box.