It seems that PayPal could have been Apple’s preferred payment process, however word has it that the talks soured which caused Apple to pull out from the talks. The reason things went south? Well if you might recall, PayPal had inked a deal with Samsung where PayPal would be linked with the fingerprint sensor of the Galaxy S5.
If you have been following the news, you’re probably aware that Apple and Samsung aren’t exactly best friends at the moment. This is why PayPal has been excluded from Apple Pay’s support and even in the developer manual, it has not been listed as an acceptable payment platform.
In fact it seemed that PayPal’s then-President David Marcus was against the Samsung deal as he knew that it would jeopardize their relationship with Apple, but apparently it was forced upon him by PayPal’s parent company’s CEO, John Donahoe of eBay. PayPal has since put out an ad in which they question the security of Apple Pay.