The fact that not even a shred of wreckage of the lost MA plane has ever shown up anywhere would lead to the logical conclusion that it did not crash.
It seems to me that the most likely scenario is that it was in fact taken over in mid-air, somehow the hijacker killed everyone (wearing a gas mask, say), and shut off the transponders. We will see that plane again when we really don't want to.
I'm not sure that's a conspiracy theory, I just don't see how the facts as we know them today leading to any other conclusion.