While stuck in Miami, I was staying with a good friend who is a pilot, a Jet pilot instructor, and someone who's expertise and experience I trust.
We had lots of long discussions about what can and can't be done to secure things "day 2".
We both agreed that the airline insustry is not going to dramatically redesign the aircraft in their fleet, nor are they going to retire working, million dollar jets that are not up to some new utopian standard.
After going around and around, we came up with the following conclusions:
1) Knockout gas - while we agreed an intruder disabling system makes sense, and is easy to do, the airline would probably face lawsuits from injured passengers in the long run, and it may not be worth it.
2) Better cockpit doors - while a good idea, the flight crew might need to use a bathroom, breeching any security a reinforced door would create. And just how much reinforcing do you think can be done without an entire cockpit structure redesign. Again, any change that requires massive refit of the aircraft is impractical.
The only idea that we both considered to be reliable and relatively inexpensive was one that would not protect the passengers but would prevent the type of "aircraft as missile/bomb" disasters we just saw:
3) Autopilot/remote pilot lockout - many aircraft flying today have the ability to land on autopilot at properly equipped airports. The flight crew and the FA's should have the ability to punch in a code that essentially engages the autopilot and locks out all on-board controls. A minor upgrade to the aircraft systems to allow this lockout feature, and also to allow autopilot commands to be sent from properly authorized ground control systems is very easily accomplished. A plane could not be controlled in this way unless the pilot or FA engaged the system (preventing ground controls that are infiltrated from crashing aircraft at will). This change, compared to the costs of the others discussed, was practical and do-able in our opinion. It may not save passengers being stabbed or blown up, but it would prevent a maniac from taking control of the aircraft.