Here is a loose collection of proposals:
interactive (editor for) graph creating: drag / drop and copy / paste
at the moment the mirrors have fixed angle and size and position. they should be mobile, allowing the user to specify just about every desired view - point ( at the moment you can move the mirrors around and zoom them, but this doeesn't change the transfo by which they get their data so far)
XML (Xj3D™, GraphML, GXL, …); VRML interface (.wrl) for im-/export
having sql face tables with n=3, 4, 5, 6, 7 … columns when creating 3D data is really ugly; there should be a possibility of better normalform design
more surfaces: for example see references (discrete minimal surfaces, Laves nets, Poeppe polyhedra, stellations of higher order, more 3 dimensional zonohedra and zonotopes, hypercubes, projections from higher dimensions), and s.th. like an '11-hole torus' with a 5-fold rotational symmetry resulting in a covering space M11 -> M3 (see [Hat02])
tetra/hepta quasicrystals higher iterations
the boards might get a nicer 3D texture to look really like made-of-wood, and the stones must have texture as well
mathematical various aspects of the graph layouting (see the section called “Calculus of Variations”)
using more advanced Java3D™ features (shared vertices data etc.)
autogenerate dual to given graph (result may be a polytope)
for all graphs use some inflation to get a triangulation like the oct_stl_II example (Coxeter reflection group with fundamental region and so on), and then do deflation of the 4 triangles around any edge to get another poly=4 graph (line graph with edges as faces) (GRAPE™ can do edge graphs as well)
again for all graphs use the paper model atlas thing (the cons/cuts from what once has been -q -s 4) to construct corresponding flat graphs with cuts as boundary edges