Team Flare is a very interesting villainous group. Their group isn't exactly about "flare", but "flair". It's a very terrible mistake in localization. I realize most Team Flare members use poison or dark types rather than fire types. An exception is Malva, but she isn't that involved in the main storyline anyway.
What stunned many people was that Mega Gyarados lost its flying type for dark. I was skeptic at first, but a super effective close combat proved that it was true.
As for Mega Flygon, I'm not going to assure myself that it's happening. However, it is rather fishy. It is confirmed that Aarune will battle you in some part of the storyline and flygon will be his ace (if beta is accurate then it'll be his sole pokemon too). Vibrava evolves at Lv45, that means the battle will probably happen between the 6th-8th gym badge. It just seems so fishy with one flygon.
He doesn't have any visible keystone, but he could be the one giving the flygonite (if there's one) to you after defeating him. A possible guess.