One thing I am thinking about with the "standard" spring solution is that this is a "cellular" system and not a particle system and I would like the "springs" to act kind of like muscles. One thing I noticed with regular springs implementations is that if I have something like a box, where each vertex is a point and each edge is a spring you also need to apply springs on the cubes diameter so that it doesn't collapse.
Joints are different however because they kind of weld the connecting objects along an axis. I would like to keep that (doesn't matter if they spin) but I would like them to have some push-pull flexibility as well as some "bending" capability.
To keep the springs from being loose, all you have to do is add not only a force as in the regular spring impl, but also a torque at the point where the spring is attached to a body.
When you setup your physical model, save the vector direction or "normal" that the spring attaches to each body. Then after each step calculate the actual vector between the spring's two attachements points, and using the saved vector, you can apply an appropriate torque which will try to twist the bodies back into allignment.