PayPal, among other companies like Square, have partnerships with certain retailers, though the proprietary solutions require a standalone app and can be more difficult to use compared to paying with a credit card or cash.
Apple dipped its toe into the consolidation of payment-oriented apps with Passbook, which serves as a central hub for gift cards, rewards cards, tickets and other digital assets, but the app's reach is still somewhat restricted. With the opening of Touch ID's APIs, Apple could potentially be testing the waters to see if a full-fledged first-party payments solution is worth the effort.