Bottom line is that Apple can't overcome the laws of economics and physics. There is always a lot of demand at the iPhone and iPad launches.
With iPad they pretty much have had it down pat since the 3rd iPad. There were no shortages, lines were short, and sales were through the roof. However, wit the iPhone it's different. The carriers have their requirements, and when you throw three colors into the mix, including an all new color that has proven popular, it makes it tricky.
At the same time, there's a limit to how many iPhones FoxConn can make. The only alternative would be for Apple to push back the release date, but that creates its own problems. First, people would have complained either that "there hasn't been an announcement yet, so I'll just get a Galaxy/HTC One/Lumia instead," or "why is it a month from the announcement to the launch date"?
From my own experience with the 4S, 5, and 5s, I think that this was handled fairly well. We'll find out tomorrow, next month, and January when/if Apple releases sales figures.
Remember that the iPhone 5 was in very short supply, as well. The pre-sales sold out in an hour, and likely just brought sales forward since the total launch weekend sales were "only" 1 million more than the 4S launch despite 2 million pre-orders.
I think the lack of a pre-order option was an indication that initial supplies were short. At the same time, Apple doesn't want to say "don't bother, we don't have any" when that's not the case at all. They are in short supply, as they always are given the initial spike in demand that comes with a release, but there are phones in the stores. I bought one yesterday in the store and so did many others where I was (with little waiting). They didn't have every color or configuration, but people there weren't pouting. They either made the decision to take what was there, or come back later when supplies are more plentiful. If history is any guide, by the middle to end of October there will be plenty to go around.
