I'm so disappointed that the 5s doesn't support Apple Pay for in-app purchases of physical goods (the payments product Stripe partners with Apple to provide). I've yet to discover any reason why except marketing/branding – ostensibly consumers would be confused that they can use their 5s for purchases through apps but not in retail stores, due to the lack of NFC. From a technical perspective, there doesn't seem to be…
The technical reason is that while the iPhone 5s has the Secure Enclave co-Processor (SEP), it does not have an Apple Pay Secure Element (SE). The SEP is a ARM TrustZone-like separate processor running a stripped down L4 derived microkernel. This manages encryption keys, the secure boot-loader and OS update signing. The Apple Pay Secure Element is a separate chip which runs a Java-Card-OS. "Cards" in the java-card-OS…
I think the bulk of my disappointment is that I upgraded to a 5s anticipating I wouldn't be totally shut out of Apple's (at the time rumored) impending launch of a payments product. Oh well, at least we get TouchID auth for apps.