Right now, every joint can be moved on one single axis. Knees, for example, can be moved on the x-axis. So, they can be bend forwards and backwards but not sidewards.

That makes perfect sense for almost all of the joints, except for shoulders. To make it more realistic, they could be movable on the y- and x-axis.

The following pictures show the difference between ...

... a fully lowered shoulder, fully contracted pec and fully contracted elbow on a usual fighter ...
shoulders_old1.bmp

... and a fully lowered shoulder, fully contracted pec and fully contracted elbow on a fighter that can move his shoulder on the y- AND x-axis (= suggestion).
shoulders_new1.bmp

If there are two axis on which a joint can be moved on, then controlling them separately would be necessary. To toggle the 2nd axis, moving the mouse to a shoulder + holding some key x might be an idea.

Though, using both axis will make fighters move asymmetrically. As far as I know, this cannot be fixed via modmaker. The following picture shows the asymmetry.
shoulders_new2.bmp

Setting the additional axis (the x-axis) to -1 instead of 1 will flip the symmetry, it won't solve the problem.

Sooooooo, this might be something you call a system change? But, the way I imagine it, using the additional axis should be optional.