I don't think the second is plausible, but the first one and third one are. A lot of airline company WTF would have happened over the absence of whatever pilots were supposed to be there. The first scenario is not impossible, though. If Usama Bin Laden and Khallid Sheik Muhammed were working for the CIA (for example), they could have orchestrated the whole thing on behalf of the Bush Administration. Considering the fact that Bin Laden was our ally against the Soviets, Bin Laden could have joined up with Reagan's vice president's son to pull the stunt. It could have happened, but I don't think there is enough backing for it. For now, it is just fun conversation.
It is interesting to think about who all is tied together in regard to Bin Laden and his buddy Ronald Reagan. Bush 41 was Reagan's vice president, Dick Cheney was Reagan's secretary of defense, and Donald Rumsfeld was Ronald Reagan's special envoy. Bush 43 is Bush 41's son. If I were tripping hard and paranoid enough right now, I might be thinking they are all just a big crime family. It is not impossible. It is just that I have to have pretty good evidence of such a thing before I believe it.