Mike, you create the picture of guns being waved around the cockpit on every flight regardless - it simply won't be like that. As has been mentioned, it is the last line of defence and was not available to any of the flight deck crew on 9th September 2001.
Had pistols been available it is just possible that the outcome would have been different. To suggest that guns in the cockpit would lead to abnormal behavioural responses is not fair or reasonable. I too am highly skilled with small arms and have used them under the most adverse of conditions.
Pilots cope with the continuing introduction of new equipment and systems and would easily handle small arms training - if it takes time to stay current so what? Better than losing all pax, crew, aircraft and high rise just because the option of arms was not available.