Well - I was going to be smart and show you that the 2013 stops better because it's lighter. Then I do the research and find out that a 2010 with a V6 runs about 4500 curb weight. Guess what - so does a 2013. So they lost the frame and didn't lose any weight?
That seems like a waste.
Stiffness requires mass. The 4th gen had a truck frame, with a lightweight body bolted to it. The 5th gen is a crossover, which means the stiffness has to be built into the body structure. Just because it's a crossover, does not mean it will be lighter, and as you found, that's not the case. What the truck frame does for you is avoid towing (and other) loads from having to be absorbed by the body. But there are plenty of "crossover" structures that can tow. Look to the current Dodge Durango. It's a crossover, and the Hemi version with HD tow package tows the same as a 4th gen V8 Explorer (around 7400 lbs). Ford abandoned this market (mid-sized SUV with big towing), leaving it to the Expedition (full-sized).
But back to the brakes, don't believe there is anything special about "Motorcraft". They get their brake pads from the same suppliers as everyone else. And given the various grades of aftermarket pads available, if you get the top-end aftermarket, they will perform well. In the case of the Explorer brakes, my Mounty's actuation has always felt soft for engagement, especially compared to my Mazda. But I can also tell you that anytime I've needed to stop fast (with our without the 5200 lb trailer in tow), it's been up to the task. It just takes more travel. But in an emergency stop, the time difference between a 3" apply and a 6" apply is nothing. You simply stomp on the brake pedal!
I had an emergency brake/lane change on the way home from Chicago last year (my fault, wasn't paying attention, glad I didn't have the camper. Full braking, swerved hard left, and just barely missed the car in front of me. Corrected to the right, and the stability control kept me pointed correctly, as we drifted into the center concrete divider. Again, completely my fault. But this 12 year old SUV kept my family safe, brakes and all.