In the past choosing a processor felt like buying a car and you really didn't have control over the rates you were charged. Swipe vs card not present and the different tiers of qualified or unqualified any given card could fall under. You could get quoted a low ball rate but it is at the processors discretion as to which tier a card falls under.
Today the choices are much easier. Paypal charges 2.9% +.30/transaction for web payments. Intuit charges 1.75% +.25 if swiped (mobile phone app included). If you don't need integrations, Square's rates start at 2.75% per transactions. The problem with square is it is a closed system without any api access. The end result at least for small merchants is more choices for an easy to understand rate structure.
New payment systems such as dwolla only charges a flat 25 cents per transaction for anything over $10. The key is the customer has to have a dwolla account that is tied to their own bank account. It seems to act more like an electronic check.