Amazon's FPS wasn't meant to be the end-all online payment system. It really seems like it was developed because so many webmasters hated paypal. And while going through amazon is a lot better than having ugly ass paypal... the users still sees a third party, which can seem unprofessional.

In my personal experience, I applied for FPS. They sent me an email asking me some more questions, then said they would get back to me in two days. It's now been two weeks.