I'm saying this in the most respectful way, but Apple is too good at marketing to claim they were caught off guard. Looking back then it really does look like it was an artificial shortage to mask the fact that the phone wasn't really that big of an upgrade. People were so focused on "Color" that they forgot to talk about "Content".
This year is different. Much bigger screen, better camera, TouchID new features, health aspect and better battery. So for the large majority of buyers who are upgrading from 4/4S/5 then the features far overshadow something as insignificant as "color".
Think about it. The iPhone got its first MAJOR redesign in 4 years and nobody is talking about it because "how it looks" means nothing compared to "what it does". IF Gold sells out then I don't think it will be far behind in backorders. (Especially since Black is really the best color on this model. Yeah, I said it.)