Hello from London! First post here. Be gentle. 
As a mechanical engineer who now works in travel (go figure) I have always had an interest in crash investigation and have read every fatal NTSB crash report published since 1967. Not for the morbid fascination of it I might add, but more for a fuller understanding of the processes that go on before, during and after accidents and the continued path of improvement beaten by investigators to try and ensure that they do not happen again.
I have to say that the CVR transcript on this particular accident (or the parts of which that have been released thus far by BEA) is one of the singularly most chilling that I have ever read. The sense of confusion, panic and despair (“We’re going to crash, this can’t be happening”) paint a vivid picture of a cockpit in disarray at the situation these three men found themselves in.
However, having read this reportin full (in French, ah google translate you are my mistress), it readily becomes apparent that a significant contributing factor to the accident sequence is indeed the design of the stall warning system/disconnect in alternate law.
If one looks at the air data from the FDR traces, you can see that from a varying combination of invalid data readings at different times (including airspeed & AoA) the stall warning goes through ‘valid data-connect/invalid data-disconnect’ sequence a staggering 12 times, with the majority of the time the warning being in an ‘invalid data-disconnect’ mode (see pg 114 Alarme de Decrocharge, brown line). The fact the lowering the nose to correct the stall (as the PNF tried) actually validated data (either through increased airspeed or decreased AoA) and so in turn activated the Stall warning is completely counter intuitive, and surely must be considered a significant contributing factor.
In addition to this is the relegation of the primary flight control in alternate law, the sidestick, to a position that is not readily visible to the other pilot, in addition to insufficient (albeit provided) warning of dual input. One only has to look at other dual-input accidents to see that mechanical linkage is not the only answer (Egypt Air flight 990 – Atlantic suicide crash - where mechanical linkage meant that one pilot was not able to override the other, though this is contested by the suicide pilot’s family).
As previously mentioned in the thread a modern airliners cockpit is already visually busy “Too much information through one channel”, so perhaps an aural “Dual Input!” warning would be more appropriate than a light on a visually busy panel, rahter than any other kind of sensors on top of sensors to make sure that the sensor’s sensor is working, all the while leaving a genuinely mistaken, and possibly terrified, PF to continue in his fatal error.
Finally a clear Attitude instrument rather than an inferred value from another display seems to the lay-man to be of utmost importance. Let me be clear, I am not a pilot, and do not understand the unique pressures of a cockpit emergency, nor the inherent knowledge gained during years in training and flight service. However, this seems to be a pretty fundamental value, as critical as airspeed or altitude. Sullenberger has been mentioned a few times in this thread, and he says of AoA Indicators “For more than half a century, we’ve had the capability to display AoA [in the cockpits of most jet transports], one of the most critical parameters, yet we choose not to do it”. See here.
Given the facts (as presented) in the document, and assuming that no mechanical factors emerge such as constant uncommanded nose-up PF sidestick input (which is unlikely given the remark “But I’ve been pulling back the whole the time” ref: CVR trans 2hr13min.40 PF (bonin) “Mais je suis à fond à cabrer depuis tout à l’heure”), then if I were to issue a crash report based on the information currently available I would conclude as follows:
Primary cause of AF447 crash:
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Pilot error due to constant, incorrect, high value nose-up input on the sidestick by PF, after the disconnect of autopilot due to icing of the Pitot tubes and loss of accurate airspeed data, leading to a climb above REC MAX altitude, followed by high altitude stall
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Failure of CRM by PF&PNF to effectively communicate actions in the period before the Captain’s return, manage available data, and designate tasks during the initial phase of the emergency
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Failure of CRM by captain to effectively take control of the situation upon his return, or to identify condition of aircraft as stalled, despite high decent rate (-10,000vft/m), high thrust (106% n1) and excessive AoA (>41deg at max), and thus take appropriate measure directly, or be delegation to recover the aircraft
Significant contributing factors
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The design of the Stall Warning data validation system leading to a disconnect/connect sequence that confused the pilots, was counter intuitive and created a situation where the corrective action was penalised by a prominent, high urgency warning (Stall Stall)
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The demotion of a key control interface (sidestick) from a prominent, visible position to one that is secondary.
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The lack of provision of significant warning cues of dual input.
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The lack of training by AF in high altitude stalls, corrective action, and appropriate troubleshooting when significant time is available (accident sequence was over 4 minutes)
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The significant operational differences between normal and alternate law in the A330, insomuch that in normal law an A330 aircraft “cannot” be stalled due to computer safeguards, whereas in alternate law these safeguards so not exist. This leads naturally to a reduction in flight control awareness (ie anything I do cannot crash this plane at altitude) in normal law.
(I feel this this is significant because the vast majority of time spent is in normal law, so it is reasonable to expect a pilot to revert to “what he knows” in a situation of extreme stress such as this accident. but this is my own subjective opinion)
Sorry for the essay, I hope you found it interesting. I would value any comments on my thoughts, or indeed any thoughts my comments provoke!