Although the human will have decided to swat the fly, the fly will not have concluded that it is about to be swatted. Only in realisation of the descending swat will the fly be able to take action. This will be some time after the 0.25 seconds of the human being's reaction time has elapsed.
Further, the fly's only sensible action is to take off and fly away. It lifts off upwards and towards the careering swat, thus negating a great deal of its performance advantage. This results in the hit-or-miss success rate we know all too well.
To initiate flight, a fly actually jumps up and backwards. With this knowledge I have been able greatly to increase my swatting success by approaching from above and behind the insects.