The most likely for me is still a massive depressurisation caused by a fire with the fire extinguishing with the depressurisation and messed up communication and navigation!
I agree - read the report on the Egypt Air MS667 772 cockpit fire, which happened on the ground in 2011. The fire was so sudden and spread so fast that the co-pilot had to immediately vacate his seat, and captain could not extinguish the fire with the cockpit fire-extinguisher(s). The cockpit was immediately filled with smoke, and the fuselage was badly holed.
http://wfol.tv/wp-content/uploads/2014/03/Egyptair.jpg
If all that happened in flight, the captain might just have had time to disconnect the AP and turn the aircraft to a haven before being overcome by fire & smoke. If the aircraft then flew on completely unguided it might have developed large phugoid oscillations which would account for the large changes in altitude reported from some sources.
After MS667 Boeing mandated modifications to the co-pilot oxygen system which had probably caused this fire. Does anybody know if the MH370 aircraft had received this modification?