Cause a pirate is free
So Mega Flygon was being considered for both X and Y and OmegaRuby and Alpha Sapphire but they couldn't come up with a good design apparently, according to Ken Sugimori in the new Nintendo Dream interview!
And with all the terrible fan designs of it I can't blame him. Flygon itself has such a basic design that to make a mega and not overdo it is asking for too much.
Maybe we'll see one in the future.