#1: You can't keep the cockpit door locked at all times, particularly on long flights where crew changes are required. Locking before passengers boards seems to be a lot of pain for little gain - "useful" highjackings take place in the air.
The biggest change that is required is to the paternalistic propaganda of our govt's that makes absolute or near-absolute security a desirable and believable goal in the public's mind when it is not. Then reasonable measures that balance cost, effectiveness and civil rights could be deployed using rational analysis.