Murkrow
Says "also" and "or something" a lot
- Pronoun
- he
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It's not just megas, the people in XY also mention how Fairy type is a new thing.
I don't think they'll explain it, the only way I can think of it is if they just move the Hoenn games later in the timeline to be at the same time as XY. There's nothing in FRLG that would contradict that; they just mention the existence of Hoenn and Lanette, not any specific events.
That, or almost all Mega Evolution is post-E4 material.
Wouldn't be the least bit surprising, considering that even in XY the only Mega Evolving pre-E4 Pokémon are your Kanto starter, the two Lucario owned by Korrina and Lysandre's Gyarados (there's also Diantha's Gardevoir but that's during-E4 technically). The vast majority of Mega Evolutions in XY are down to the Mega Stone hunt that you can only conduct after becoming Champion.
As for the Fairy-type, let's not forget that GSC refers to the Steel-type as a ~new thing~ and then not only did RSE have Steel-types, but FRLG had them as well (ie Magnemite, Magneton).
I highly doubt that they'll mess with the timeline just to accomodate some technicalities which they've never even bothered with accomodating in previous remakes.