It seems to me that the general consensus among our northern brethren is for mugo, while those more southern tend to prefer JBP. One of the major differences between the two is that mugo is an alpine tree, growing at higher elevations and more northern climes. The JBP is a warmer-weather tree that grows at sea level. Perhaps the misunderstandings between the two have more to do with the fact that it takes more heroic measures to keep JBP healthy in colder winters, and more heroic measures to keep mugos happy in extreme summer temperatures.
With enough knowledge of either species, one could get good results, as proven by folks from all over. So perhaps personal preference should have more to do with how much we are willing to do in the off season to keep our tree healthy and vibrant. If I decide mugo is something I want to work with, I am going to consult with folks who have a great deal of experience with them, always tempering what they say with the knowledge that my climate is a bit extreme in the summer months. The same might go for those in northern latitudes for Japanese black pine.
White pine, scots pine, mugo pine, austrian pine...All have their place depending on where they thrive. I'm in no hurry to attempt to keep large numbers of tropicals here, since I don't have a heated greenhouse or awesome sunroom to keep them happy. It gets too cold here in winter for many tender species without extreme care. I also won't be doing much with larch for the same reason. It gets far too hot and dry for too long here. Larch do not thrive (if they even survive). More's the pity. The same might be said of varieties of pine depending upon where one lives. The more extreme the climate, the stronger the inclination might be for a particular species. Some species may have a wider adaptability than others, but why swim against the stream? Work with something that likes your climate.