An additional case that I know about, the Tenerife airport disaster: http://en.wikipedia.org/wiki/Tenerife_airport_disaster

Quoting:

  Speculation regarding other contributing factors includes:
    The flight engineer's apparent hesitation to challenge Van Zanten
    further, possibly because Captain Van Zanten was not only senior in rank,
    but also one of the most able and experienced pilots working for the airline.

  As a consequence of the accident, sweeping changes were made to
  international airline regulations and to aircraft... Hierarchical
  relations among crew members were played down. More emphasis was
  placed on team decision-making by mutual agreement.

Wouldn't the Air France 447 crash be an instance where a low ranking officer did not notice errors & was given too much control of the plane, resulting in the deaths of many people?

It sounds like both co-pilots were having mental blocks while operating together in the cockpit. With Bonin stalling the plane, while Robert is unable to figure out why the plane was not responding like he thinks it should & the insecurity of these events leads him to defer to the captain, who is not present.

I am not sure specifying a hierarchy would have helped so much in this case, but the example crashes given in this thread don't explicitly show that the hierarchical structure was the sole cause of the crashes, there were many contributing factors which lead up to both.

Your link doesn't say that there isn't a clear chain of command, it says that there should be a culture that allows professional disagreement or calling to attention. Just because the captain is declared top dog doesn't mean that protocol demands subordinates must remain quiet.

BTW, who is commanding the plane (by inputs) and who is commanding the crew are entirely separate questions. I think one of the serious issues that MUST be addressed here is the issue of conflicting commands to the plane.

Two options.... 1) Place all controls between the pilots so they can easily see what eachother is doing or 2) Place a selection switch and indicator that allows a pilot to unambiguously take control of the plane and disable the other input, or to keep them in linked mode where they move together and provide tactile feedback as to what the other input is doing.

What happens if they're fighting each other?

Then they have to fight! You can't delegate responsibility to the "system" to resolve such a fight. A fight is a fight. And if it's happening, you can't automagically get rid of the fight.

At least there's feedback, and you can immediately see what's happening! In the current configuration, Bonin's stick inputs were nearly unknowable to the other officer.

Yes, the link doesn't say that, but research further and you'll find that the concept of a hierarchy is what CRM aims to eliminate. It's the First Officer's job to take the flight controls from the captain if the FO thinks the captain is doing something dangerous. Not to ask for permission, but to immediately do. This goes against the concept of a hierarchy, but is why they put two sets of controls up there.

I think you'd still do better to have a manual selection of which input is commanding, with an option of having both sticks linked and moving together.

Deliberate selection of inputs would be best. Maybe a switch in the middle that both selects and displays which input is active?