Pushed a couple updates to the skin-modifier branch: output-face attributes and non-square skin limbs. These have both been frequently requested.
The skin modifier UI now has a material selector. It shows all the material slots of the active object, and the selection will be used for all faces output by the skin modifier.
Similarly, all faces will be either flat-shaded or smooth-shaded depending on the selection made in the combo box.
The second change, non-square limbs, means that you can now scale the X and Y axes of vertices independently. It uses the usual scaling mechanism, so pressing (for example) SKEY, XKEY will work as expected. Note that rotation is still entirely automatic, so you can’t choose the exact angle of a non-square limb, but should be OK for many cases.
Code is in the usual place.
Update: as suggested here, I’ve removed the material selection in favor of simply using the object’s first material slot.