This is a great question and I don’t have a good answer for it. I do, however, have a few uneducated guesses.

• Regulation: innovating in payments requires working with regulators and privacy concerns, and any new concept introduced requires a lot of convincing. This requires a lot of energy, taking focus away from innovation. By the time someone is done with their first payments company they are so done with the field that all of their valuable experience is never used.
• Features, not products: most of the attempts to innovate in payments have not been viable products but rather improvements to existing options, Stripe included. Innovating in payments requires deep industry understanding because most of what you do in payments is under the hood. As a result, companies start with some novel idea, and then meet the realities of the business and wither away quickly (related to the previous bullet).
• Stagnation in large players: once you’re big enough in payments, you’ve made so many compromises and adaptations to your system to work with regulators, acquirers, collection companies and other players in this fragmented market that you’re both worried about innovating since stuff break all the time, and unable to innovate because of your current solution’s limitations.
• High barriers to entry: finally, as I keep noting, the two huge barriers in setting up most payment services are access to capital and user adoption. Most companies fail these, way before they can bring any innovation to market.

That said, I think that Braintree (payments company) and Stripe (company) are making interesting, innovating moves in the gateway segment and Square, Inc. is reinventing UX for offline purchases (and, a plug, at Klarna we are doing something new in eCommerce payments). There are things to look for.