Rear Brake, my opinion why it is weak

Here is my opinion with some history:
I use to have a 09 ninja 250 which I traded in for my nc700x. On the ninja, I almost always used the front brake with little back brake but when I practice emergency stops sometimes I lock the rear brakes. Once I got use to the nc700x, I started practicing emergency stops with it and notice how really bad the brake was. The rear brake was so bad, I had to use a lot of weight on it when stopped on a hill not to roll backwards. First dealer said it was normal and I just need to get use to it. Didn't believe it. I then noticed there was very little movement for the back brake pedal. I took it to another dealer and he diagnosed it as glazed brakes. This now made sense. I bet most dealers do not check back brake pedal travel when setting up the bike for the customer. So the rear brakes get over heated and glazed when new. To fix this, you could use sand paper on disc and pads or do what I did, be very heavy on the rear brakes every once in a while but don't use it so much as to overheat them. Once I started doing this over the past three months (3000 miles) the brake pedal has more travel and works a lot better. It still not as good as my ninja, but it is a very big difference from what it use to be which was about useless.

I thought my rear brake problem was basically as you have opined. But, after fooling around with the brake for a while I now have a different opinion. I think there is something wrong with the caliper that puts the pads at a pretty strong angle to the rotor. This causes the caliper to bind on the guide pins when the brake is used, without much braking force generated. The "cure" is the same as what you found to help. Using the brakes hard starts to wear the pads in with a taper. Eventually, you end up with a condition in which a lot less binding is generated and more braking occurs. Still not right but almost usable.

Look from the rear - does the pin that holds the pads in look like it has an angle to the caliper? Mine does. Depress the pedal, does the caliper seem to have an angle to the rotor? Mine does. Finally, does your caliper slip back and forth easily on the guide pins when the pedal is not depressed? Mine does not, or hardly at all. If you take the pads out is one worn on the radial "inside" and one on the radial "outside"? if so the pads are being pushed into the rotor at an angle.

I think Honda has put a lot of defective rear brakes out in the world on this model. I can see where a dealer might not know about them yet. But to say "you just have to get used to it" is just hoping a potential problem goes away. My local dealer is as flaky as they come, and I didn't buy my bike there, I've little hope of getting any satisfaction from him.

I think we should follow up on this - Honda will issue a recall if the problem is a defective caliper. How one goes about this I don't know.

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Here is a picture of my set up. The out of square angle of the retaining pin is about 2.5 degrees. I don't know at this point if it is the brake stay or the caliper that is causing this.