With regard to the “secondary flight plan” programmed into the box 12 minutes before contact was loss:

What if the crew updated the “secondary flight plan” flight plan from their t/o airport as their return airport for an emergency to a new alternate emergency airport for the over open ocean water portion of their flight route.

If you look at a map of Malaysia (or even go to Malaysia Airlines own website) you will see that the best suitable alternate for the over the water portion of the flight was turning to the left 90 degrees not returning to the t/o airport. In the northern portion of Malaysia there are several airports that are suitable for a triple7 to land, are serviced by Malaysia Airline and are closer then then t/o airport or Vietnam (obviously until they got closer to Vietnam).

As for the Waypoints that the aircraft supposedly flew too between the water peninsula of Malaysia and Indonesia...were these waypoints the start of a STAR into one of the northern emergency airports they selected? Or were these waypoints programmed into the secondary flight plane for descent purposes only for an emergency landing from FL350 down to say the STAR waypoint altitude, safe altitude or approach altitude.

Meaning the crew was just thinking ahead for when they coasted out over the open ocean in the middle of the night.