As for me, I first decide upon which shopping cart to use, then I see which processors it supports.
Think about customers. When they come to your store, what they see first? Not how your processor works for you, no. They value the shopping facilities (how user-frendly is their cart). So, that's why cart-choice is major, and processor choice is second choice.
I would rely on POPULAR processors. That's again for customers' sake. The customer feels good when he knows his payment methods. I mean, everyone knows PayPal, Authorize.Net, GoogleCheckout - right?
Let's say, you choose some less-known name for processor. But the processor guarantees tons of security. But the name is worse-known. From my personal guess, the customer would rather choose popular name, not the unknown. It's just our nature, that we feel more comfortable with familiar things. And I doubt, that your customer will stop ordering, go to Internet to learn about your unknown processor, and then, all-reassured, come back to complete the payment.
So, the transaction fees are important, of course, but not the crucial point. I would pay a bit more for each transaction, but be sure I WILL have those transactions
As for affiliate or recurring billing, or reports - yeah, it's nice when gateway has these additional services. But in my case these features come with my shopping cart. So, not really necessary from processor side. This is again about cart choice
