I am sure the Shimano brakes would be beþer, but I just did a brake pad upgraxe on my Formulas and the stopping is improved and the noise greatly.diminished.
Check here for various Kool Stop models approriate for Formula brakes:
Another choice of organic pads would be these:
http://www.amazon.com/Organic-Semi-Metallic-brake-pads-Formula/dp/B00H6WXENA
The Shimano M506 brakes that come on the 2016 X are fantastic...so much so that I see no reason to replace them...except with another set of affordable M506 brakes. Do a little research - they are recognized as THE best bang for the buck.
Aren't the shifter and the remote also attached to one of the brakes? That is, it's possible to change one of the brakes but not the other side. I'm very tempted to switch out the rear brake in any case.
Even if the shifter/remote are attached to the brake lever, if you are switching to another brand of brakes, you can cut off the Formula brake lever and use the cut off section as a clamp. Then you can use any OEM brake system that you would like.
I got a right brake lever that was no good from my LBS and used the cutoff portion so that I could clamp my brakes independently from the shfter/remote and make the hand positions comfortable AND be able to actually see the control panel;.