First, let me qualify my statements by saying that I work in an HD dealership service dept.
The rotors on a tri-glide are IMO too small, but do have a large advantage over 2 wheeled iterations as the rotors do have the extra mass of the hub flange to act as a heat sync.
We have seen the main problems (e.g. noise, wear, and general lack of performance) to be related to parking brake adjustment. The adjustment, at the caliper, not at the lever, manually moves the inboard pad to clearance correctly from the rotor. As the pads wear, which is rather quickly for the inboard pad, this clearance increases. When the brake pedal is depressed, and the inboard pad is farther away from the rotor, more effort is required to do the same amount of work, because the outboard pad is contacting the rotor and offering resistance to the pedal, but not really applying braking action. We are performing a parking brake adjustment sometimes as often as 2500 mile intervals for some customers who use the rear brakes primarily, and they all remark on how much better the rear brake action is when we are done. All of that being said, the biggest thing tri-glide owners can do to prolong good braking action from the rear is keep them clean. Cleaning the braking system regularly clears debris that scores rotors and pads, and helps the pin sliders work more effectively, which will let the outboard pad help out more. regular adjustment of the parking brake mech., either by a dealer or yourself may keep this braking action more to your liking. I also understand some changes have been made to the 2011 rear brakes, but we have yet to see one.
I don't know if any of this helps, or if it's all been tried, but maybe it can shed some light on the subject.