So you are into the conspiracy theories huh? :)
Bush senior didn't finish the job in 91 is for several reasons. One, we learned a lesson from the panama invasion in making a country's leader a primary target (It's a fact that the US military never knew at any one point where saddam was.) Second, Bush didn't want to get involved in another Vietnam style war. At the time that was probably the biggest fear of the gulf war, when would it end? So clear, concise objectives were laid out, which brings me to my next point. Third, our main object was to get Iraq out of Kuwait and as a result of that destroy it's military. The motivation behind it was basically the oil. If Iraq took kuwait and had access to all of that money to build up it's military even more, what would be the next target? Saudi Arabia, and we weren't going to allow a huge supplier of american oil be threatened like that. (We built that base in Saudi Arabia after the gulf war for that purpose, to be a deterrent force to an Iraq invasion) So the overall objective was never to defeat Iraq, occupy it or kill Saddam, it was simply to cripple Iraq's military to the point it would be no threat to the middle east and mostly Saudi arabia.
As far as the government allowing 9-11 to happen, it's far fetched but certainly not impossible. Some say Rosevelt knew of the attack on Pearl happen back in WW2 but allowed it to happen anyway since that was the only way to get us into the war and get the country motivated to fight a war.
And as far as little green men running around in the desert at area 51, you're guess is as good as mine ;p