The placement of some of the armature joints relative to the mesh is off. This results in problems when the joints are posed any distance from the default pose. For example, the shoulder joint is placed far too low and this results in gross deformation of the mesh between the neck and shoulder when the arms are lift up and out to the side. I haven't learned how to properly edit the placement of armature joints yet but I did manage to produce this illustration of the effect of shoulder joint placement:
The shoulder joint on the left side has been moved up, the right side is the current default.
Please try your best to ignore all the other problems on the shoulder on the left, they are a result of my trial and error blundering in Blender, the relative point is that by placing the shoulder joint near the surface, as it is in the human body, you eliminate the downward deformations of the shoulder surface between the shoulder and neck.
Am I right that the placement of the armature bones relative to the mesh is done by MakeHuman so the fix should be done in MakeHuman? I'm willing to work on improving the armature placement if someone familiar with the MakeHuman code will figure out how to incorporate the changes into MakeHuman. Would exporting the default on startup model and armature to Blender and fixing it there provide what's necessary to incorporate the changes in MakeHuman? I'm not sure whether to work on the default armature or the CMU armature trying to use the CMU mocap files with characters with the default armature results in the neck position being screwed up? Will armature positioning changes done on one translate over to the other easily?
Thoughts?