Are there any benefits/downsides to ordering the iPhone 4S from the Apple store versus the Sprint store?
Not really. It depends on whether you want to deal with Sprint or Apple. When Sprint does FTB, then it makes sense to go with Sprint because you get it early. however, I don't think Apple is allowing FTB.
Both sites will start pre-orders on the 4S tomorrow (10-7-11) and are going to have the same deal/promotions as well as rules and regulations concerning upgrades or new lines of service. So like pharaoh0 said, "It depends on whether you want to deal with Sprint or Apple."
pre orders are online not in stores. its not a reserve you order it online and its shipped to you by the 14th or you can go to a store (Apple or Sprint) and get it there.
i think i would rather preorder with sprint if i was pre ordering the first day at 2am ct. if you have one of the first orders you will get it first with the FedEx located inside of Sprints wharehouse. after that i would go with apple cause they normally update you and tell you the ETA better than sprint. Sprint will just continue to tell people we will try to get it by 15th or 16th.