I think it's becoming pretty clear that in the Apple stores, the only interface available to the Apple employees for setting up plans and activating the phones is going to be the iTunes interface and whatever changes they have made to that. It doesn't sound like they're going to have access to the AT&T system directly.
Now I think in the old one on launch day, the only types iTunes could handle were new AT&T customers, people buying the iPhone as a current AT&T customer on a contract (with no new subsidy) or just adding it to a family plan, and people who passed the credit check with no deposit. Other people it would send to the store or offer the prepaid.
So I guess it depends on how much they have changed the iTunes interface- how many new situations they have programmed it to handle. It sounds to me that if you don't fall into a real easy upgrade situation, i.e. a new customer, a current customer just upgrading one current iphone to one 3G, or just adding a new one to a family plan, that you should just plan on going to AT&T. At least that sounds like the safe plan to me.
Even though AppleInsider posted this it's still not clear how they will handle the difference situations and it's getting too late in the game so I am just going to stick with going to AT&T to be sure I get one Friday:
"As mentioned previously, Apple retail employees will not be able tell whether an existing non-iPhone AT&T customer is eligible for upgrade pricing before beginning a new iPhone 3G purchase transaction, so customers should determine this on their own first. However, customers unsure of their upgrade status can still upgrade to iPhone 3G at Apple retail stores. Once a purchase transaction for these customers has begun, Apple's EasyPay handheld systems will indeed tap AT&T's account database at a certain point to determine the price to charge the customer for the iPhone hardware. The customer just won't know ahead of time unless they check their account status online, go to an AT&T store, or call AT&T customer service."