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 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...