Someone is to blame
The fundamental flaw I see in all conspiracy theories is the assumption that "unanswered questions = someone is hiding something".
The truth is that there has never been a criminal investigation that didn't have at least a few unanswered questions. In criminology, the official conclusion of an investigation is that theory which best fits the available facts. For any other theory to be considered it must explain more of the available facts than the official conclusion.
So many conspiracy theories fail simply because they have more holes in them then the official conclusion (if 9/11 was a fake then where are all the passengers from those planes?)