I've watched a lot of Air Disasters episodes about crashes where pilots thought auto-pilot, auto-throttle, auto-trim were "in control" but they weren't (or vice-versa) due to some innocuous pilot action - like bumping the go around setting. See: https://en.wikipedia.org/wiki/China_Airlines_Flight_140
From a Human Factors engineering perspective, it seems that it should always be obvious who has control of the various flight controls. One simple option is to put light strips on each physical control (yoke/stick, throttle, trim) to indicate who "has control" - the pilot or the flight computer. If the throttle levers light strip is green, auto-throttle has control. If the light is off, the pilot has control of the throttle. This may seem a bit simplistic for normal aircraft operations but in times of high stress such a simple system might make a difference - preventing a crash. Lights like this would of course need to adjust to the ambient light so they're not glaring during night yet visible in bright daylight.