Gizmodo posed this question to AT&T and was told that "there will be no limiting difference between the two stores", unless you are a business customer.
If you are a business customer you should purchase your new iPhone at AT&T rather then the Apple store.
For those business, or enterprise customers, they will get their iPhone 3Gs through their normal IT processes. This will ensure that their business can take advantage of any corporate discounts that may apply.
Gizmodo was told that business activation will work one of two ways...
If your company pays the bill for your iPhone 3G: Your IT department will provide you with iPhone 3G, just as it does any other device. Then, all you need to do is sync it to iTunes from your computer and it will be good to go. You do not need to go to an AT&T retail store.
If you pay the bill and are reimbursed for it by your company: Buy the iPhone in an AT&T retail store. Give the salesperson your company's contract number with AT&T and the device will be activated.