Bush has a socialist, big government mindset. He may also be waiting on approval from the UN powers that be.
The smallpox vaccine is left over from the 70's, some older, and so due to the age of the vaccine it is currently being tested by The National Institute of Allergy and Infectious Diseases (NIAID), a component of the U.S. National Institutes of Health (NIH). Production has its problems as well, the FDA has found violations of quality control standards in the manufacturers, such as Merck who had their plant closed down and lost the contract due to QC violations.
As far as guns in the cockpit, Bush signed the Aviation Security Bill, which included provisions for arming pilots, but Mineta, Ridge and Magaw were obstructions in implementation, seems that is now changing, with the recent passage of H.R. 4635, the Arming Pilots Against Terrorism Act which orders the the TSA "to develop and implement a two-year 'demonstration period' during which a limited number of volunteer pilots would be armed". It also helped that Magaw was ousted from his post.