MB 2012 GLK brakes

Yes, it's all been done by MB mechanics

Unfortunately it's been two different MB dealerships running into the same issue. I can tell when the rotors need replacing, the car shakes when the brakes are applied (about 3000 miles after replacement). Different dealerships, different mechanics, no answers. MB replaced the parts 3x via warranty, the 4th time the dealership only charged me his cost for the parts, no labor (about 40% of what I paid in total the 1st time). This just makes no sense...there has to be another outlying cause.

Your, "car shakes when the brakes are applied", because, almost certainly, the brake rotors have warped. Rotors warp because they have been exposed to excess heat. Unless you are racing your GLK on a race track the probable cause of the rotors overheating is that the brakes are being continually applied while driving. I have never driven a GLK 350 but my daily driver is a GLK 250 (similar vehicle, different engine). I have noticed that the brake and gas pedals on my GLK are closer together than on other vehicles. I have also noticed that my foot sometimes presses on both the brake and gas pedals at the same time. Constantly applying the brakes, even slightly, while driving will overheat the rotors, increase brake wear and decrease fuel mileage. I suggest that you have someone follow you in another vehicle to see if your brake lights are on while driving down the road. If they are on, you have just confirmed the source of your problem. Then make a conscious effort to move your foot over to the right a bit more on the gas pedal so that there is less possibility that you are applying pressure to both pedals at once. Wearing narrower shoes, if possible, would also help. That should solve the problem. Your Mercedes service folks have been REALLY remiss in not suggesting this possibility to you.