I think people are putting to much thought into how they're gonna implement/explain Fairy-type/Mega Evolutions etc. I mean, we all know it's a new mechanic, GameFreak knows it's a new mechanic, why do they need to make an explanation in the game when we know outside of the game why they implemented the new typing?
I mean, remakes can rewrite what happened in the original and give it a new history. They did with HG/SS & FireRed/LeafGreen. They will rewrite it so that Fairy-types were either always there or that they were also 'recently discovered' in Hoenn. They aren't going to have this complicated reason for it. At the end of the day, these are games aimed mainly at children. They aren't going to expect children to be reaching for an answer as to why they're there. They're going to play the game and have fun playing with it.
As for Mega Evolutions, unlike Fairy-type, it wasn't claimed to be 'newly discovered' in X & Y (or it was an I've forgot). It's not something new, it's just that no one has seemed to know about it or use it in the games. I personally think they're going to have either a previous character or maybe a brand new character come in and be like 'hey- I'm from Kalos, and this is the deal with Mega Evolution'. I mean - Mega Stones could have always been there just never found or no one knew what they were so they never thought they were anything special.
TL;DR: They don't have to have a big complicated reason for it. You may think you 'deserve' an explanation but I think it's highly likely you won't get what your looking for.