>>23030638-Salamence (Drake + being a Hoenn pseudo-legend > just being cool Flygon)
-Latios/Latias (necessary for Soaring > just being cool Flygon)
-Altaria (Lisia contest bullshit)
-Sceptile (Hoenn starter > just being cool Flygon)
-Rayquaza (yes fucking Rayquaza witht he whole Delta episode business > just being cool Flygon)
all 6 had actual reasons for why they had priority to get mega evolutions.
That's already 6 fucking Dragon Megas in one game who are iconic to gen III and more relevant.
The only one they could have skipped of those is Altaria as they invented her trainer character for ORAS in the first place.
I mean even if we assume they intended to make Aurunes role the same level of importance as Lisias, we can see how the decision between the two was made easier by the fact that a similarly inconvenient case shows up if you look at it from Flygons actual main types perspective, new Ground Megas:
-Swampert (Hoenn starter > just being cool Flygon)
-Camerupt (Magmas signature poke > just being cool Flygon)
-Primal Groudon (it's on one of the boxes ffs > just being cool Flygon)
Flygon is as relevant as say... Aggron or Walrein.
Sure, they're all cool 3 stage pokemon iconic to Hoenn, but relevant to the actual story of ORAS they are not. Hence why Aggrons mega wasn't saved for ORAS and why Walrein didn't get one.
Then why Glalie, Pidgeot and Beedrill got ones? For at least some basic semblence of type diversity across the new Megas..
Get over it. Flygon will join soon enough anyway, and with even the slightest luck, there will be new toys for it and some original thought invested in making a Mega for it, rather than it having to stick with Levitate and just boosted stats as probably would have happened if it had gotten a Mega this time.