Media speculation to this point is that some very large monsoonal thunderstorms (55,000 feet high) may have played a role...based on the confirmed report of the pilot requesting an alternate route during flight.
Proof, I guess, will be if they find debris in daylight. The Java Sea to the Soutn China Sea is somewhat narrower waters than in the pervious aviation troubles there. This should allow for easier search, particularly if the plane was south of Borneo as they seem to think. Irony that the parent airline is again based in Malaysia.