Jolly is the best possible nature, as it is important that flygon not be outsped by his fellow dragon types, and the many base 100 speed Pokemon, so that he can ensure he gets the crucial first move. However, flygon's attack is a little underwhelming, but there's a moveset than can fix that.
Flygon: choice band
Evs: 4 hp 252 atk 252 spd
Fire punch/Stone edge
Choice band boosts flygon's attack by fifty percent at the price of limiting him to one move.