I have the new Honda Pilot this week. Very roomy, very good outward visibility, plus good mpg considering its size. But the ride is unsettled and it's not fun to drive. I feel like I'm driving a minivan more than in the others. Also, while the Pilot is quieter than past Hondas, something about the interior (even the top-of-the-line Touring Elite) seems downscale or institutional. It's the best appliance.
The Highlander has more of a truck-like feel than the Pilot, less minivan-like. But it has considerably less third-row legroom. I'm working off memory here, and might drive one again while I have the Pilot.
The Durango drives the best of the three (it's really unlike anything else in the segment) and has perhaps the most comfortable seats, but as you note it probably won't be as reliable. I think most of the problems being reported involve the electronics, all of which tie into the infotainment system introduced with the 2014. It's possible they've finally debugged this for 2016.
The Mazda CX-9 is an old design at this point, but it remains among the sportiest crossovers (this being very much relative).
I also liked driving the Kia Sorento considerably more than the Pilot and the Highlander, they've done a great job with the chassis tuning and overall refinement. But it has less passenger and cargo space than any of these--it's really in between size classes. So size might rule it out for you.
My main concern with any crossover except the Ford Explorer and Ford Flex is that there isn't enough luggage space for more than a few bags behind the third row. The Fords have a minivan-like well that opens up space for another couple of duffels. But if you don't need the third row when traveling then no problem.
For those who do need cargo space behind the third row, a minivan will have far more space back there than any crossover. You might want to at least look at the Kia Sedona. To me it looks and drives sportier than the Honda Pilot or the Toyota Highlander. But if you need AWD, then it's not an option.
Drive a few of these and let us know what you think!