I, like many others in the retail industry, was hoping the iPhone 5 would include an NFC chip that enabled a mobile wallet. In previous postings I've discussed the possible business case and the foreshadowing of Passbook, but it wasn't meant to be. A few weeks ago I was considering all the rumors, and it suddenly occurred to me that it wasn't in Apple's best interest to support an NFC chip. Yes they have patents in this area, but perhaps they are more defensive than indicating new development.
Steve Jobs wanted to always win, but more importantly he didn't want others to win at his expense. It drove him nuts that Windows was more successful than MacOS, and clearly he was bothered by Samsung and other handset manufacturers copying the iPhone. But he was most angry at Google for their stewardship of Android.
If the iPhone 5 had an NFC chip, who would benefit most? Google Wallet is far and away the leader in NFC-based payments via mobile phones in the US. Even without Steve at the helm, Apple isn't going to do anything to help Google. Plus Apple doesn't like to do things in an open way -- then they lose control. For example, you don't see iPhones with expandable memory, replaceable batteries, or USB connectors. Adding a standards-based NFC chip just isn't in their nature.
So I don't think Apple is holding back on the NFC chip for the 5S or 6. It just isn't going to happen unless they can figure out how to prevent others from benefiting from it.
All the other handset manufacturers will use NFC as a differentiator, which may be enough to keep Google and Isis afloat, and of course Square and PayPal aren't betting on NFC anyway. This isn't the end of alternative payments, its just a major speed bump.