Uhh, dude Flygon simply can't fly to a legendary pokemon.
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Here is the list of Pokemon who can learn Fly: Salamence Rayquaza Crobat Zatu Skarmory Taillow Swellow Wingull Pelliper Vibrava Flygon Swablu Altaria I made Swellow and Flygon Learn IT.
The strongest dragon type in pokemon Emerald, Sapphire and Ruby, is the legendary pokemon Rayquaza. In terms of non-legendary pokemon, both salamance and flygon are strong dragon types.
Nah, Pokemon that you can get more than one of in games without cheating or trading aren't legendary in my book. I have heard someone call the Dragonite family legendary and Arcanine is actually called "The Legendary" Pokemon, but I think that's more for the TV-series.
yes it can