I'm a late comer to this thread, but I wanted to chime in that my 2011 3.0 FWD does the same thing. I have approximately 135k on it, but purchased it at 50k. At 70 MPH I can feel it pulse in and out as I travel down the interstate. I can accelerate it up to 90 MPH and it does not miss a note. In cruise, it pulses.
Most of the items mentioned in earlier posts I have considered as potential fixes. The only item that I have done is that I have cleaned my throttle body, for other reasons. It had no effect on the pulsing, but did fix the off-idle acceleration problem.
The only other thing that I thought might be variables:
Is the transmission torque converter is going from lock-mode to unlock-mode?
Many modern cars have a torque converter lockup mode in order to achieve better fuel economy. I am not certain that this transmission is so equipped, but I would guess that it is.
Is the fuel pump changing pressure levels?
Is there a brief vapor lock in the fuel rails on the engine under the high temperatures of a continuous highway drag of 20 minutes or more.
By the way, I had a similar issue in my old 2006 Taurus. I bought that car at 55k and ran it up to 130k. It had a completely different 3.0 liter cast iron push rod V6 and different transmission.
I would really like to get this fixed. I like my Fusion a lot, but things like this are definitely detractors to the fun of driving it.