1) Price keeps changing. We've had the underlying price change multiple times over the past few years. This can make it very difficult if your margins are thin. I see your price guarantee, and I think it's a good idea except for one thing: what if your underlying service providers (Authorize, Samurai) change their prices?
2) Still waiting on better reporting. This is a good article on metrics to track: http://www.readwriteweb.com/cloud/2010/09/6-saas-metrics-you... A recurring billing provider should have most of the info to provide these. Sure, I could write it all up in excel, but I have other stuff to do. Make my life just a teeny bit easier.
3) Vendor lock-in - As others have mentioned, portability is a big concern. If we had to switch away from Authorize.net it would be a nightmare to get everyone to re-input their card details. You should make it absolutely explicit what new customers need to do in order to achieve portability. This means knowing your underlying providers, but trust me, your customers don't know them. The reason they're coming to you is because they want to offload the burden of knowing and managing all that.
I wrote up my reasons for going with Chargify a while back: http://peachshake.com/2010/06/15/saas-subscription-billing-o...