There is one Paper out there that says that few "warped" rotors are actually warped, they say it is more like uneven brake pad deposits on the rotor, which are grabbier on certain parts of the rotor and slippier on other sides, causing that pulsating pedal feel.
There are strong opinions on either side of this argument. Here is a link, form your own opinion.
http://www.stoptech.com/technical-support/technical-white-papers/-warped-brake-disc-and-other-myths
Since reading the above paper I have taken care, after a hard stop or anytime I know i have heated both rotor and brake pad up in the super hot zone, not to leave the front brakes clamped hard on my rotors( use Emergency brake instead to stay stopped, and I have not had the pulsating pedal since.
There also seems to be some correlation in pulsing pedal to driver habits. Some brake late and hard and keep a lot of pressure on the pedal waiting for a red light, more than which is needed to hold the vehicle stopped. These people seem to find their pedal pulsating more so than those who brake earlier, less hard, and only exert enough pressure on the pedal at a red light to hold the vehicle immobile.
Fewer shops carry disc brake lathes these days, because new chinese rotors take less time to install. Yet quality can be all over the board on these. I had a horrid set of Duralast rotors which lasted 10k miles before the bearing races started spinning in the bores, which were also machined too deeply. Those cheap Chinese rotors really cost me a bunch more in the long run when I had to replace both bearings(SKF) and rotors( Brembo) at the 10K mark,
One mechanic I trust will not put new rotors on vehicles without turning them first on the lathe, and he claims that this has reduced come backs by 90%.
Certainly other suspension issues could be attributing factors to the OP's condition, such as worn suspension components, but it is likely the rotors are warped, or have uneven pad deposits on them, and turning them on a lathe is the remedy, and perhaps driver awareness of the cause can help to keep them at bay in the future.