A NY Times article documents the ridiculous way that doctors get paid.
But in suggesting alternatives, why does the article not mention the most common sense way to pay doctors? Based on how much time they spend with a patient, and on how much time they spend working on the patient's behalf in the patient's absence.
Of course, this would still encourage them to perform unnecessary but time consuming medical tests and procedures, but it still makes more sense than paying based on how many checkboxes they can check off on an insurance form. Pay by the hour is the most difficult method to game. And if patients have a percentage-based co-pay, time-based pay will give them an incentive to not waste the doctor's time.
With time-based pay, doctors would be willing to talk to you on the phone, saving patients the hassle of going into the office for minor issues that could be easily resolved over the phone.