I can't speak to these, but I can speak to D5000 vs D7000.
First, though, the 39-point system in the D5500 is, I think, the same system as in my D7000. My D5000 had an 11-point system. When I was looking at upgrading from the D5000, my primary considerations were better high-ISO performance and higher burst speed for continuous shooting. AF never crossed my mind; what did cross my mind was the question, "Why the hell would anyone ever need 39 focus points???!?!"
My first outing with the D7000 demonstrated the better operation of the new AF system: it focused faster and more accurately, with the same lenses, than the D5000 did. My first air show with it, a couple of months after getting it, showed me why you need more focus points.
I'd tried Continuous AF with 3D tracking on the D5000. The manual explained it, the setting was in the configuration, but it didn't work. I think it was a combination of the system not being fast enough, and the fact that more of the viewfinder was empty of AF sensors than had them. They were just too far apart, and an aircraft being tracked could too easily slip between the sensors. That first air show with the D7000, though, it was flawless. Absolutely flawless. Over 1100 frames, mostly in Continuous AF with 3D tracking, without missing focus once! So the number of focus points matters, as does the speed of the system.
I haven't shot with a camera with the 51-point system, but I do get instances where the 39-point system falls short by not covering the top and bottom edges of the frame. It's nearly complete left-to-right, but only three rows of sensors. The 51-point system fills a lot of that space in.
Summary: D7000 focused the same lenses faster, and almost never "guesses" the wrong direction like the D5000 would, and 3D tracking worked.
The D5500 is that system, and the D7200 is almost that big a step up from there.