Before we knew the iPhone was real, the common wisdom was that in order for Apple to make the experience something of acceptable quality, they'd have to own or at least rent the cell network. Take a look at this iPhone activation and sync video. This is clearly an Apple experience, simple, clear and elegant. Apple is doing what it does best, and AT&T is doing what they do best. This is how every business partnership should be.
Doing activation and sync away from the store allows Apple to control the "out of box experience" which I think is key. You don't get an iPhone without your calendar, contacts, pictures, music and videos. If you did get a phone without all the above personalized data, the first time experience would be decidedly different. From a logistics and spontaneity perspective it also allows people to buy the iPhone quickly, cash and carry, and allow them to do the longer part of the process in the comfort of their own home. No pressure, everything at your own pace. This is designing an experience, not a phone.