OK let's break this down. AT&T pays Apple a fixed price for every "AT&T" iPhone that is sold via any Point of Sale. It does not matter if you purchase from AT&T, Apple, Target, Walmart or BestBuy. The price is much higher then the $199 subsidy price on the 16GB model.
AT&T uses the subsidy model to get you to lock into a two year service commitment and they allow you one hardware subsidy normally between 18-24 months. They make their profit a little each month so the $250 profit is not recovered in the first 6 months as you hoped.
Those are the basics. Now, when you pay the Early Upgrade Fee of $250 you are helping to offset the cost that AT&T has to pay for your "additional" device. You already used your first device subsidy when you purchased your iPhone 4S as an "Early Upgrade" last year before your two year service commitment was complete. Again AT&T pays a flat fee to Apple so that's why they want every "AT&T" iPhone to be activated on AT&T. It helps offset the cost per device they have to pay to Apple.
There is no Free Lunch with the subsidy phone model here in the US. The device costs the carrier much more then the $199 you want to pay. If you don't like this model just purchase at the "No Contract" price and you are free to purchase as many devices as often as you want.
Also remember that your existing 6 month old iPhone 4S shoud be at least worth $250
Dave