1) None of the flight instructors of the hijackers who took flight lessons said they were good students. In fact, most of the hijackers who took flight lessons seemed remarkably inept at flying.
2) None of the hijackers had ever flown a large jet before, even according to the official story.
3) The hijackers had to take over the cockpits then fly hundreds of miles without the help of autopilot. This is not a trivial feat.
4) The hijackers must have used either visual geographic landmarks for navigation or portable GPS instruments. The first feasible but is not an easy feat, particularly for someone not from the US. The routes the hijackers did choose were not well suited to using key geographic landmarks-- for instance the planes going to the WTC could have navigated down the Hudson river fairly easily, or down the Long Island Sound, but they didn't do this. I don't know how feasible it is to use store bought GPS instruments on a plane, but I supect it is not trivial.
5) Not only did the hijackers have to steer the planes in rather extreme turns, when they had never before flown a large jet, but they also had to descend at least 20,000 feet-- from cruising position to near ground level. It is essentially impossible to believe that they could do this, using only manual controls with their level of experience, without losing control of the plane.
6) The hijackers had to make very tight, controlled maneuvers to strike the targets perfectly. The odds of this being done three out of three times by untrained jet pilots is miniscule.
7) Flight data recorders were recovered from the Pentagon as well as from the WTC, but the data has never been released. In fact, the black boxes recovered from the WTC weren't even acknowledged by the government-- just by the firefighters who worked at the clea up site. This strongly suggests the authorities are hiding key details about the flights that would show the hijackers weren't flying the planes. Even the full cockpit recording from flight 93 has not been released to the public, again suggesting the authorities are hiding key details. The government has only released parts of the flight 93 tape that conform to their story of the passenger revolt and cockpit storming.
8) Remote control of airplanes is a fact, and remote control drones have been used extensively by the military. NORAD has used such drones as practice targets in live-fly exercises. In fact, there was such a live-fly exercise being run by NORAD on 9/11.
First, we have a fairly strong case that the hijackers simply were not physically capable of flying the planes into the WTC towers and Pentagon.
Second, we have a cover-up of the flight data for the planes that crashed into WTC towers and Pentagon.
Third, there is a good alternative explanation for how the planes could have been piloted if they were not piloted by the hijackers.***
On the other hand, what evidence is there that the hijackers WERE flying the planes?
None really. The only "evidence" for the idea that the hijackers were flying the planes is the (naive) disbelief that the government would never lie and would never carry out such a monstrous act. But the fact is, the government does monstrous acts all the time under the general rubric of "covert operations".
***Of course, one other explanation is that the airline pilots were doing most of the flying under orders of the hijackers. However, this defies belief for several reasons, since we have to believe that, a) the pilots had no idea what the hijackers were going to do (particularly after the first plane crashed into the WTC), b) the pilots were able to control the plane but then did not fight the hijackers, or try to crash the plane, when the hijackers wanted to take control, c) the pilots could not surreptitiously warn air traffic control of the hijackings by pressing 7500 on the transponder, d) the hijackers kept the pilots from talking to air traffic control by radio when called, even though that would have forestalled air traffic control recognition of the hijacking. With all of these things taken together, it is fairly unlikely that the airline pilots were doing the flying after the hijackers took control of the cockpit.