No Gym Leaders have so far, so it's not likely that the rest will. Maybe the E4. And tbh, it depends on the Mega. A lot of them are Meh at best.
Hardy would get Mega Aerodactyl or Mega Tyranitar-both don't change much from their normal versions-so the same ways to beat them still apply. MAYBE Mega Aggron if Ame bends the rules a bit, but it's not that good.
Titania might be a problem with Mega Mawile, Mega Lucario and Mega Metagross.
Amaria gets Mega Blastoise and Mega Gyarados (meh) and Mega Slowbro (slow, and easy to defeat if you know it's coming).
Saphira is unlikely to have Salamence as it's the signiture mon of the E4 Dragon member, so she MIGHT have Mega Ampharos or somesuch. Maybe Megazard X, which can be OHKOd by an Earthquake.
Faeries have Mega Mawile that might be a threat, and Mega Gardevoir.
Flying has MegaZard Y that might hurt.
Very few things that can't be dealt with, and as I said before, the odds of anyone pre E4 who's not named Lin having a Mega are almost nil.