All Roads Lead to "MIHOP" (Made It Happen On Purpose)
1) "Wily terrorist theory": The idea here is that the Bush administration/US government was competently and actively trying to stop 9/11 from happening and just failed because the terrorists were so smart/tricky/wily.
This can be ruled out by the fact that if the terrorists were THAT smart and wily, they would have struck again in the US by now.
2) "Caught Off Guard Theory" (related to the Competence theory): the Bush administration/US government WAS actively and competently trying to stop 9/11 from happening, but were simply caught off guard because of government SNAFUS and bureaucracy. After 9/11, the Bush administration competently fixed all these problems.
The major problem with this thoery is there WERE high-level warnings, making it hard to argue the Bush administration was truly caught off gaurd. Further, it is highly improbable that the Bush administration could have fixed so many bureaucratic problems in time to prevent another attack.
3) "Al Qaeda shot their wad" theory: this goes that Al Qaeda put everything they had into 9/11 to make it successful, but had nothing left to follow up with, and then they didn't figure that the US was destroy their bases in Afghanistan and so they were ultimately defeated by poor planning.
The problem with this theory is that a terrorist organization has to have some grand strategy, and it was incredibly idiotic if they did not "plan ahead". If they could plan 9/11, they could plan what would happen afterwards.
4) "Al Qaeda just got very lucky" theory: this goes that Al Qaeda put together 9/11 but didn't know if it would work-- then it worked spectacularly on every possible level but they had nothing planned to follow up with, and then they didn't figure that the US was destroy their bases in Afghanistan and so they were ultimately defeated by their tremendous success.
The problem with this argument is that Al Qaeda was FAR too lucky on 9/11 (even by the official story) to have succeeded by random chance. Further, it is absurd to imagine they didn't have a follow up plan should the attacks succeed.
5) "Al Qaeda set a trap" theory: this is the idea that Al Qaeda mainly did 9/11 to lure the US into a attacking a middle east country, such as Iraq, and then Al Qaeda would be able to mount a world-wide Jihad.
The problem with this argument is that how would Al Qaeda KNOW if they could truly lure the US into attacking some country like Iraq, but more importantly, and more importantly why would the Bush administration fall so easily into this trap since it was such an obvious trap? Further, the "trap" theory clearly goes against the idea that Al Qaeda didn't predict a devastating reply on their bases in Afghanistan.
6) "The Bush administration was incompetent" theory: this is a favorite of Democrats and mainstream liberals, as it feeds into their meme that the Bush administration is simply incredibly lame and stupid, topped with a dash of evil.
The big problem with this theory is that it simply can't explain how the incompetent Bush administration has prevented another 9/11 from occurring. Further, it is hard to believe anyone could be so incompetent as the Bush administration has seemed-- incompetence has always seemed to me to be a lazy attempt to rationalize what the the Bush administration has done. Additionally, it is clear that the Bush administration is NOT incompetent in many things, so it makes little sense why they would be incompetent on such a major thing as "national security".
7) I haven't seen this point put forward, but you could propose some combination of the above-- for instance, the Bush administration WAS incompetent to allow 9/11 and Al Qaeda did get very lucky and had no follow-up plan-- or the Bush administration WAS incompetent to allow 9/11 and fell into Al Qaeda's trap to attack Iraq.
A combination theory makes somewhat more sense, though ultimately these theories fall short, I think, for the same reasons we can rule out the individual theories.
8) "Let It Happen on Purpose"-- basically the idea of the official 9/11 story except that elements of the Bush administration/military/government just allowed the attack to happen and did not actively stop any attack-- as the attacks would further their goals of starting wards in the middle east. This is 9/11 conspiracy theory "lite", and many people seem to fall onto this idea after doing some basic research into 9/11.
The problem with this theory is that it is simply impossible to imagine that people in power who would allow a major attack on US soil would let it go without some sort of control on the attackers, and controls on the attackers mean that you are making the attacks happen the way you want-- which is MIHOP.
All this is putting aside LOTS of evidence and LOTS of very compelling physical evidence, and just looking at the mainstream 9/11 political picture from a strategic point of view.
Ultimately, all the theories fail on basic logic grounds, and point to MIHOP.