Guys the real issue is dipstick Ken Sugimori, since 5th gen he's been on a crazy on/off amount of artist block. He's even admitted in interviews that he had Mega-Flygon planned since basically day 1 of XY, but because he couldn't draw it "write" and didn't wanna pass off his dream project to someone else he made himself and the rest of us suffer. Hell it's why Garchomp's in it when it should have been Cynthia's Mega, or could be one of them, for DP Remakes. Basically same with Wallace outside Sky Pillar, he was suppose to have a Mega, which shockface probably was Mega-Milotic, but again idea got scrapped and yes to your rage probably why Mega-Audiino was added in to keep the number up.
Seriously like said if anything blame Masuda and Sugimori, cause I bet the latter had artist block on Milotic and because it was getting too late they scrapped both. While it sucks, and oh trust me it sucks, there's a bit of hope.
Lucario and Garchomp have already been special pokemon and got Mega-Stones, in fact one of them being the first Mega-Stone you ever get in XY except Day 1ners who got Torchic, so by process of elimination Milotic, Gastrodon, Togekiss, Roserade and Spiritomb are pokemon Cynthia has had in 4th Gen that could get Mega-Evolutions.
While I think ALL of them could get one easy cause there some of the other 4th gen mons that best stand out, with the demand for Mega-Milotic and the fact two Lucario and Garchomp Megas have already been gimmicked out, feel like Mega-Milotic might be best for a Mega for Cynthia. If not her then them having another contest star for the Super Contests and/or maybe as a gift from a visiting Wallace.
Flygon's still a bit iffy, I mean when you fuck up and don't get a design out for two games straight with a third new-Mega filled one on the way next year, I wouldn't be surprised if Sugimori finally breaks down and gives it to his protege, or works with his protege on it after the others are like "Dude wtf?"