We've had so many theories since the crash about what may have happened... from lightening to new composite materials on the plane delaminating in flight to a storm so bad that it broke the airplane apart.
In fact, it crashed just because the pilots couldn't fly the plane in a way that anyone with a PPL would know how to do (when stall warning occurs nose down full throttle!).
So basically the mystery of AF447 crash is that... the pilots crashed an aircraft that was in perfect working order. Yes, it was in perfect working order, failed pitot tubes doesn't mean the plane was not in PERFECT working order.
The pilots incompetentness are to blame for the death of all those poor helpless passengers.