MarkT:
With large step changes where the error is close to 180 degrees the error quaternion
is under-determined. This means rate-limiting step-changes in the input quaternion
is a good idea.
MarkT,
Do you propose an increased sampling rate to reduce step changes? Appreciate the comment on the variability of torque effects based on configuration. Per jremington's advice, I am testing the waters of inverse kinematics, which I vaguely remember from my academic background. I believe the biggest challenge was the formulation and efficacy of the inertia matrix, which seems a similar challenge to the one you present with the aircraft control axes.
Without a test rig I am figuratively spinning my wheels, since I'd rather do so literally. I will start in the 1-D case and build upon the linear assumption.