Hey Sean -
I'm a member at PN/MP and have played each many times over the past five years. There really are some big differences between the two. You've identified some and here's my take...
MP's greens definitely have more interior movement, especially if their speed is similar to PN's. Putts break far more than they read, whereas at PN they seem to break less than it looks. I can't think of a course I've played with more severely breaking putts, especially at just moderate speeds. You can pretty much hide the cup in the middle of each green and make them extremely difficult to access unless you are coming up at them from a very narrow range of angles. Kyle Franz was given lots more freedom to shape and contour the greens at MP whereas at PN all he could do was add a limited amount of material to the existing surfaces, and it definitely shows up in the complexity of each green from a putting and chipping perspective.
You mentioned that you didn't think think much of MP 13-16. I, and many of us who play these courses regularly, believe that the final five at MP is one the most interesting and attractive finishing stretches of holes in the area. Fairway placement is crucial depending upon cupping locations. Further, each of these holes typically favors a shot that's shaped in one direction and then an approach that's shaped the other way.
MP is a fantastic hickory and ground game course. Even though at first glance PN seems more amenable to that style of play, MP is probably more intricate and interesting in this respect. There's a reason why a major national hickory event is held at Mid-Pines every year. While many of the greens are elevated a bit, they can pretty much all be accessed by working shots off the bumps and hollows 10-30 yards short of each green. #9 is a perfect example, one that Jay Mickle has pretty well mastered. Even thought it's a short par-4 and you can almost always wedge it in, often the better shot is something that's bumped in along the ground from just right of the left hand green side bunker.
I prefer MP's routing as it's an interior course whereas PN is routed through a residential community. It's far more intimate a routing, an easier, quicker walk for sure with tees typically right on top of the preceding green. A feature that we all love is that MP can be played in any number of loops. My wife and I love playing 1,6,7, and then 12-18 late in the afternoon. 1-4 is a nice loop that brings you back to the clubhouse, and there are a bunch of other opportunities to bounce around. And the view from around the 6th green is incredible, as from that one area you can catch a look at more than half the holes on the course and really see how the course flows in all directions.
Last thing -- played at a similar yardage, MP is definitely the more difficult of the two courses. During our club championship or pretty much any other event where the two courses are used, the scores at MP are pretty uniformly 2-4 shots higher.
I can say lots of positives about PN as well and really enjoy playing it. But if I have to split 10 rounds, it's definitely going to be 8/2 or 7/3 in favor of MP.