My primary motivation for boosting Mathcad's graphics capabilities was to do a ball and stick model based on some regular and irregular polyhedra such as the icosahedron and the truncated icosahedron. I originally used the 3D scatter plot but had the problem with the extraneous lines when I tried to connect the points. It simplifies matters if you can let the computer determine what lines to include in the table containing the link point indices. This was accomplished by first finding the nearest neighbors of each point and then entering a line in the table if the index of the end point was greater than that of the initial point. This avoids plotting duplicate lines.
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