It all just looks like innuendo, or Bible Code or Nostradamus-style coincidences.
Besides, the two aircraft don't have that much of a difference in fuel burn. A professional 777 captain could certainly figure out how far the fuel on 200ER could get him.
Of course the FS data doesn't prove anything, but I can't see how the aircraft could have ended up where it ended without any input from either pilot. If both pilots died you would certainly expect a more straight flight-path.
In addition, the waypoints of the multiple track segments all have identical values for certain incidental values - something that is highly unlikely unless these segments were all recorded in the same session. This makes it extemely implausible that these segments, which are consistent with what is known of the aircraft's dog-leg track, were created accidentally.
That being said, you can throw out all the simulator evidence and still be left with a very strong case, from the reactivation of the Inmarsat equipment and the turn to the south, that someone was controlling the airplane an hour after it could have reached the airports at Kota Bharu or Penang.
The initial flight path matters least.
He mightn't have known which day and route would present the opportunity, which would also have to coincide with the right frame of mind for him to execute this operation. His opportunity might have depended upon who was assigned co-pilot on the day.
So, whatever initial flight path he took was outside of his control. What was under his control was the part we are trying to understand now - the rest of the voyage, and the destination.