Salamence because it totally outclasses Flygon on a competitive scale in terms of versatility and power. Flygon was prized in Adv for EQ/RS resistance which allowed it to be a decent counter to Ttar.
Since the advent of D/P however, Garchomp completely outclasses Flygon in all stats (except a tie in Special Attack). Flygon stopped being a primarily offensive pokemon, it now has Roost/U-turn to be different from Garchomp, but 80/80/80 defences don't cut it. The need to counter Garchomp has also introduced an almost mandatory rule for a team to carry an Ice move that could end Garchomp's sweep, which in turn directly affected Flygon.
Salamence however gained a lot on D/P with Draco Meteor. The amount of powerful physical attackers this generation also boosts the value of Intimidate and allows Salamence to function as a physical wall given Fighting resistance and access to Roost.