I should probably point out that I'm a little obsessed with them- I have a few hundred Buckyballs (various colors and stuff), as well as a couple thousand of the Zenmagnets. The big differences really come in when you're trying to make something delicate or with a larger structure.
One major issue is consistency- the sizes between colors or even individual balls in the same set varies quite a bit. If you create a flat plane (one height, whatever length and width) or magnets with both the Zenmagnets and the Buckyballs, the Zenmagnets will be level all around while the Buckyballs have different sized. This causes some to bulge out, making that level plane actually quiet bumpy looking.
The other problem is that the coating they use over the actual neodymium is very cheap. The longer you own the Buckyballs the more of it breaks off. The Zenmagnets are going to last quite a bit longer, and not break down in your hands just because you let them snap together too hard.