First of all, in my part of the USA (Detroit, Michigan suburbs), the Rite-Aid stores are absolute *****-holes and are not kept nearly as clean as the competing Walgreens and CVS stores. Secondly, Walgreens is the only PARTNER with Apple in this whole venture, of the big three pharmacy chains. So, given those two facts, why on earth would I even consider shopping at Rite-Aid? They already have disgusting stores with rude employees, and now they won't let me show off my cool iPhone 6 Plus with ApplePay to my friends and family? Yeah, I think my business belongs to Walgreens from now on.
Furthermore, as a physician, I think I may go out of my way to recommend my patients go to Walgreens. As it stands, there is a Walgreens within walking distance of my office (unlike the other two), AND ApplePay works at that store like a charm, as I happily discovered both yesterday and today!