Not sure what you mean about wearing out a set with pad still left, but if you are referring to the wear indicator, they aren't exact. The wear indicators on all pads are there for use as a guide and are not exact.
If you are referring to uneven wear, like one side is gone with pad still left on the other ... that is usually caused by sticking or corroded slide pins. Sometimes they will wear uneven for no apparent reason, just happens.
If you are talking about the same pad wearing uneven ... that is usually caused by misalignment the last time they were installed or debris on the mating surfaces.
If you use the rear brakes like I do, mine only last about 12k miles, so two in 25 ain't bad.
The fronts pulsing, well that very well could be warped rotors. If they are badly warped, replacement is the only way to get rid of the problem. But you might try taking the fronts apart, cleaning and wire-brushing the pins and surfaces. Lightly grease the pins before reinstalling them so they slide easily but not so much that the grease could get on the pads or rotor. Also clean and lube the caliper sliders the same way so that they move back and forth freely. If the calipers are frozen in place, even a light warp in the rotor will be magnified. No rotors are absolutely perfect, that's why the calipers need to slide easily.