There is considerable circumstantial evidence to suggest that remote control technology may have been used to override the planes's controls. It is highly unlikely that flight school drop outs managed to carry out the precision maneuvers on 9/11, and it is even less likely that an expert Egyptian or Saudi pilot would have picked the recently strengthened, under construction, almost empty section of the Pentagon as a target.
The side of the Pentagon that was hit was nearly empty -- and the location for an ongoing major construction project to strengthen the building against such an attack. The plane's trajectory would be extremely difficult for a novice pilot to perform (unlike the much simpler approach to the Twin Towers). This fact makes the official story of "novice pilots" less than believable ...
The first plane that went into the towers passed over Indian Point nuclear power station, on the Hudson river just north of the New York City suburbs. The alleged "al-Qaeda" is described as wanting to do as much murder and mayhem as possible, yet chose to avoid a target that would have caused unbelievable devastation (how would all of New York city, or New England, be permanently evacuated? This question is a good reason to shift from nuclear power to renewable, safe, decentralized energy sources).
The towers were hit near the top, before everyone had arrived at work (most of the people inside the towers managed to escape). While this is not any consolation for the victims, their family and friends, and everyone who suffered psychological trauma from watching helpless on TV, it is a fact that the attacks could have been much worse.
Modern passenger jet planes have multiple alarms to call air traffic control in the event of a hijacking. This is similar to banks that have multiple alarms that can be discreetly activated to sound a silent alarm to call the police. It's probably not public knowledge how many there are on a plane or how they work in a bank - nor is that probably priviledged information the point. It's difficult to rob a bank due to excellent security in most bank franchises (the best way to rob a bank is to buy it first, and use some of the loot for campaign contributions to compromise as many politicians as possible). Similarly, plane hijackings were extremely rare in the US before 9/11 due to adequate security, including the Air Force domestic air defense system. However, on 9/11, none of the commandeered planes sent out any alarms that they were being hijacked. If the planes were actually equipped with remote control technologies - which are not theoretical at all - it would have been easy to ensure the transponders would be automatically turned off once the external controllers "hijacked" the plane. "Crossing the Rubicon" by Michael Ruppert cites mainstream media reports about radar "injects" used to insert fake blips onto radar screens during war game exercises that morning - which would have made it difficult for military officials not part of the conspiracy to find the real, hijacked planes (since the planes would not become "stealthy"