All good ideas. I'm sute implementing them would have stopped precisely zero out of zero terrorist attacks on US planes that actually succeeded since 2001.
So, since security is lax (like we didn't know already) and there haven't been any successful terrorist attacks on planes in the US since 2001, what precisely would your methods achieve?
If the answer is saving lives then I contend there are better methods to save lives. Your methods sound expensive. Terrorism isn't a significant threat. If you spend the money on road safety you'll likely save a lot more lives.
Anyway point by point:
1. Require a special ID to use commercial airplanes. The ID would require that you are on a list and they know who you are... transport on the system is not a right. If you're a suspicious person then the system might just say "take a bus". By all means open the system up to due process so if you think you're on a ban list then you can fight that in court. The system might also flag certain people out for more security when they show up at the security gate. So you'd still get to be on the plane but you personally would be going through extra security because the system doesn't trust you.
Except no one was in any doubt who the 9/11 terrorists were. They all used their real names because why not? They had no prior terrorist activity and didn't exactly care about their future reputation becoming tarnished.
2. Give flight attendants and pilots some defense training. That includes possibly giving them weapons. I have no problem for example with the pilot having a gun. If he can fly the plane into a mountain then he can be have a machine gun for all I care.
He can't though, not in the US. The US has already required two people to be in the cockpit for years precisely to stop this kind of thing.
3. Upgrade the computer security on those planes. You shouldn't be able to control the auto pilot through the entertainment network accessed by wifi. That was fucking pathetic.
OK firstly that never actually happened as far as anyone can tell. Secondly having better security is equivalent to a highschool teacher telling you he always makes sure he has the best brand of condoms when dealing with pupils (with apologies to XKCD). The solution is an airgap, of course, not upgraded computer security.