Timid nature is +Speed -Attack, it means Flygon's Speed Will grow more but it's Attack will grow less. Here's 2 nature's I recommend on Flygon:
- Adamant (+Attack -Sp.Atk)
- Jolly (+Speed -Sp.Atk)
Flygon can learn Earthquake and it get STAB from it And it Can learn Dragon Dance for Speed and Attack boosts so it Depends on stats.
EDIT: Before the Release of Pokemon Sun and Moon, Flygon couldn't learn Dragon Dance. If your playing any of the gens 1-6, then use Swords Dance with a Jolly Nature. In Gen 7, Flygon can learn Dragon Dance so use Dragon Dance.
Hope this helps :)