4. Transparency not working with multiple transparent objects
From Kevin Rushforth:
The basic problem is that transparency is inherently an order-dependent operation. For the rendering to be correct in all cases, all triangles must be rendered from back to front. In cases without a lot of overlapping transparent objects, you can usually get good results by rendering all of the opaque objects, freezing the Z-buffer, and then rendering all of the transparent objects. However, this sometimes has the side-effect of causing transparent objects that are further away to look like they are in front of transparent objects that are closer. Turning on the Z-buffer (by disabling DepthBufferFreezeTransparent) fixes this, but creates other problems.
Without sorting your geometry--and breaking it up in the case of intersecting objects--there is no solution. In Java 3D 1.2 we have proposed new blending modes that will allow you to blend transparent objects in a truly order-independent manner, but with the side effect that you get an additive effect where two objects intersect.