So it seems that we have three basic issues (and possibly more but not as prevalent):
Pilots can crash planes. Someone can just be suicidal, be part of an extremist/terrorist group, can have a vendetta against someone or just thinks might as well take more down with me.
Passengers that get into the cockpits. I know that the cockpits are locked and pilots are armed but on a lot of flights there is opportunity.
Using technology to override aircraft autopilot.
So what is the long-term plan to keep these things from happening from a technology point of view? Is there anything in the makes that will help solve these issues? I foresee some sort of technology that requires some sort of dual sequenced unlocking to allow a pilot to make a certain % deviation from flight plan.
Note: There have been a lot of answers here that basically say "nothing is being done" and offer up reasons why. To use the recent incident of a pilot dropping a plane into a mountain as an example, my main question surrounding that is, is there a technology that would see that the pilot was well off course? Is there technology that would see that the plane had a high risk of crashing? Is there technology that would prewarn flight control (even if it were a few minutes)? Is there technology that flight control could override plane and right the ship that is going into the mountain?