I'd love to use Stripe, however the 2.9% fee is a total deal breaker. I'm currently using Payflow Link (by PayPal and Verisign) and I pay a flat rate of $20 a month plus 500 incl monthly transactions. I can get more at 0.10 per transaction. And after that it's all done with my Merchant account, which I've been able to negotiate down below 2%.
When you're doing hundreds of thousands of dollars (or more for you big guys) in credit card transactions, eating 1% just for a friendly API is a huge turnoff.
Please Stripe, prove me wrong and provide an external merchant account option!