i don't understand. you say you upgraded. That should be a brand new phone. the serials should all match. That right there would have me in the store saying this isn't the phone from the box, fix it.
You keep saying replacement. Did you're 4 get broken and you went in for a replacement? In that case they don't owe you a new phone. But if you went into a store, paid the cost of a brand new phone as part of your 2 year upgrade the phone should be new with a matching box, and you didn't get all that. Personally, i'd go into the store you got it from and sort out what you got. I see in the post above it looks like you went to best buy. I've never bought a phone there so i don't know all they do or how they work but, me i'd never have walked out the door without being sure.
i have no clue if they can do this but maybe you can call your carrier and see if that number phone has been activated before. If it was you'd know it was refurbished. If not you that may mean nothing. Maybe they give it a new serial when it's refurbbed. i don't know. That's the only thoughts i got.
I think the OP upgraded on Dec 9 by going from the 4 to the 5. On Dec 14, the OP had to get the 5 replaced for whatever reason. The concern is that he may have a refurbished phone. The OP is upset because if the phone was bought from Apple, then the device could have been returned and swapped for a new one. However, instead, the OP went though the Genius Bar. Now, the 5's serial number does not match the one on the box. (I only understand this because I was in a similar position back when the devices first released and my carrier didn't have any more in stock to swap out.)
OP, it's okay that the 5 is a replacement unit. When you go to sell, just explain that you received a new replacement from Apple. You can also disclose that you were told that the phone is new and not a refurb. Try not to let it bother you too badly.
There is nothing you can really do. I had a similar thing happen with me. I wanted to get the 5 back from Apple and just send it back to my old carrier and return to my 4S. (There were issues provisioning any 5 with my profile on the network.) However, the devices are boxes up and shipped out to wherever every night or whatever so I couldn't get it back.
Also, I don't think there is any way you can return the device and get your money back because you don't have the original device.