sorry to resurrect a dead thread, I had a similar experience of uneven/almost shuddering feel after replacing the rotors and pads. It was weird because there was none of that when braking harder only when normal pressure is applied. I took apart the whole rotors and pads and found nothing wrong but discovered that the pins were not sliding very smoothly, one side was almost ceased completely. I took them out cleaned and applied brake pin grease and what a difference it made. The braking is progressive and smooth like it was when I first bought the car.
I have changed brakes/rotors on all my cars for the past 15 years but none needed pin lubrication, so I learned a lesson here and maybe someone can learn from my mistakes and lubricate pin every time.