Well, it depends on the opponent, not just the Pokemon. I mean, against a DD Salamence, a Choice Scarf Flygon could possibly 2KO Salamence with Outrage, even with Intimidate. Flygon can still Revenge Kill Salamence if needed. Also, A Choice Scarf Naughty Flygon will always OHKO a Salamence using Draco Meteor if it has 0 HP/SDef EVs with a hindering nature, as long as it outspeeds it.
Most cases though, Salamence would beat Flygon, seeing as it has a higher Attack stat, Equal speed, a better ability, better Special attack, more resistances, and being an all-around bigger threat.