Skinned Knuckles had an article looking into this a few years ago. As I recall, their conclusion was that there is no good reason to prefer one way or the other. Both positive and negative grounds have been used by a lot of different manufacturers over the years.
At one time, I understood that it had something to do with minimizing corrosion at the connection to the frame, but I now understand that that is bogus.
Just from a physics perspective, it's hard to imagine that the electrons care about which direction they are being asked to travel through an external circuit. It is important that the electrons in the spark plug spark be jumping from the hotter, tip material to the cooler, base material, but that can be arranged well enough with either battery grounding arrangement.
Steve