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 are cryptographically "personalized" by the payment network (VISA, AMEX, MasterCard) with per-device keys and the device personal account number (DPAN)--the tokenized device only credit card.
This is the same java-card + payment network personalization that physical chip-and-pin cards, Google Wallet and most other NFC payments use.
So my guess is that the Payment Networks were not comfortable using the Secure Enclave Processor and preferred to reuse the same technology used by chip-and-pin, with a separate Secure Element chip.
Source: https://www.apple.com/privacy/docs/iOS_Security_Guide_Oct_20...
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.
I thought Apple was pretty notoriously bad about this sort of thing?
Find out which flagship Android phones have an official 5.0 ROM and let us know.
Is this 'tokenized device only credit card' the same concept as the Point-of-Sale seeing a unique CC # (generated) for the transaction? (What I believe is one of the selling points for Apple Pay). Are there other products that do this?
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 anything holding the 5s back. The A7 has a secure element/"enclave" like the A8 (a cryptographically secure place on the SoC to store payment tokens, fingerprints, and the like), and the 5s has an A7 and the TouchID sensor.
EDIT: The secure element is in fact distinct from the secure enclave. agnokapathetic explains below.