Theshadow
It's a lot of words but if I read you correctly your thesis boils down to:
(1) Plane runs into problems gradually.
(2) Autopilot deals with problems gradually
(3) gradual problems accumulate until autopilot is overburdened and disconnects.
SURPRISE!
(4) befuddled pilots who didn't even know anything was wrong get disorientated, or confused, or lose spatial awareness, etc.
(5) Plane crashes.
With respect, that's not exactly a new thesis or a new problem. I don't know if it's true in this case; it wouldn't surprise me given the facts we know.