The plane was hijacked and there has been contact with Malaysia/China/USA. One of the conditions for hostages to be held safely is that the Authorities do not make this public.
This would explain:
- the otherwise unbelievable delays and pure misinformation by the Malaysian government. Stalling for time.
- the fact that they did not publicly do background checks on all passengers until recently. They already know who the hijacker is. Now that there is pressure because of elapsed time and that people are seeing holes in the story, they need to be seen to be doing something.
What makes this implausible:
- it still does not explain where the plane landed and has been hidden without trace in the interim (perhaps they know - NW Pakistan, NE Afghanistan maybe, and just can't get to it without harming the hostages)
- it would be a diplomatic nightmare to have countries using their assets in a futile search when Malaysia already knows what has happened. (On the other hand, if they took 20 countries into their confidence then they would definitely have had a leak by now.)
- talking of leaks - I am sure even if it was a tightly held secret that they were in hostage negotiations, someone would have made it public by now. That's just the way things are these days.
EDIT: Formatting