I've said this before, and I'll say it again. Lock down (physically rearchitect if need be) the cockpit so during flight no one gets in, no one gets out. Toilets and rest areas are included in this secure area. There must be no physical way to travel between cockpit and cabin while in flight (i.e. pilots enter via separate exterior door). It's awfully hard to take over a plane if the cockpit can't be compromised. This requires training of pilots to understand that preventative losses are acceptable losses. Second, each plane should have a dual-key activated defensive system to knock out people in the main cabin (via oxygen decreasing or some chemical agent or some other solution) which requires both pilot and the relevant authority on the ground (military? FBI?) to activate.

In the long run it will be cheaper than the security theatre of late, and more effective.