Logistically, Apple stores can't activate phones. Have you EVER bought a phone in a cell phone store and went through activation? It takes a while. There's no way they could manage that with the amount of people who'll be waiting.
Apple has said that you'll need an iTunes account to setup the phone - but it didn't mention activation. Still, they warned to have your account ready. That's one scenario.
The other is that you just activate through the phone. Rumors I've heard from in store are that you'll activate online. We recently added a phone to our family plan on Cingular. The number was setup in the store, but before I could use the phone, I had to answer automated questions through the phone "do you agree to an extended two year contract? Push 1 for yes..."
After a bit of that, the phone was active and I setup my voice mail. So, I'd imagine the iPhone would be similar.
The bigger question is HOW you transfer your number. I think activation is going to be easy. Transfers are the big issue since you can't move your SIM. The iPhone doesn't allow you to put your own SIM in it - this is done as a theft deterrent.
I think it all goes back to having to have an iTunes account and having to activate the phone through iTunes. If that part is true, then God help us all if EVERY person who buys a phone at an ATT store has to set up an iTunes account on the spot! That's scary.
this is most likely the correct answer. but i don't forsee ATT reps activating the phones in-store. They will sell you the phone and you take it home to your machine and activate it. However, that does leave the number transfer issue up in the air. I think mav was right about this when he said specifying your number will probably be done by ATT either over the phone or via internet.