Nintendo Dream held an interview with Game Freak’s own Ken Sugimori, Shigeru Ohmori, Shigeki Morimoto, and Kazumasa Iwao, all of whom worked on Pokémon Omega Ruby and Alpha Sapphire. During their time together, Sugimori revealed the sole reason Mega Flygon doesn’t exist: artist’s block. It could go without saying that this is possibly the reason why many of our favorite Pokémon don’t have Mega Evolutions, but it’s incredible that something so minor can have such a lasting effect on a game’s biggest new improvement.
Sugimori: For Aarune, he needed to have a Pok♪0mon that could use the moves Fly and Secret Power, which are perfect moves for finding Secret Bases. And the only Hoenn Poéemon that wasn’t used by a key character that fit that criteria was Flygon. It does not Mega Evolve, but I really like Flygon.
Interviewer: Key characters often carry a Pokémon that can Mega Evolve, but Flygon is an exception, right?
Sugimori: Flygon has had the potential to have a Mega Evolution since X/Y, but we were unable to complete a design and so it was dropped from consideration.
Source: PokéBeach