Each Dragon Pokemon have their strenghts and weaknesses, both with their own niches that separate them enough to be uncomparable. Flygon is a Speedy Sweeper who's objective is to KO the foes Pokemon while taking the least amount of damage, while Druddigon's objective is to sponge as many hits as possible while retaliating with powerful attacks.
That being said, who is stronger?
Both are Physical Attackers, so let's compare the Base Attack of each Pokemon.
Flygon: Base 100 Attack
Druddigon:Base 120 Attack
Druddigon wins in the Attack catergory. However, Flygon's Base 100 Speed allows it to outspeed several Pokemon and fire off an Attack whereas Druddigon will typically attack last.
So, in my opinion, Flygon is the stronger choice as a Sweeper as it's decent Speed and usable Attack allows it to score KOes like Druddigon but while taking the least amount of damage as possible.