In an interview with Nintendo Dream magazine, series character designer Ken Sugimori stated that the character Aarune was given a Flygon since it was capable of learning both Secret Power and Fly, which were key to finding Secret Bases.
He also revealed that the reason Mega Flygon was not included in both Pokemon X & Y and Pokemon Omega Ruby & Alpha Sapphire, was because Game Freak had trouble trying to complete a design, so it was dropped.