No explanation that makes pokemon that previously didn't have the type now getting it works because of fairy not being affected by dragons. If I fight a marrill right now on Black or Black 2 with my Haxorus one outrage will kill it.
Maybe there will be some sort of relic in the game. We'll call it the Magical Relic. Nobody knows why it exists or what powers it contains. It is an enchanted relic that has odd effects on certain kinds of Pokemon. A few Pokemon from the Kalos region, after exposure to this relic, began to develop the Fairy type. Once Pokemon from other regions began migrating to Kalos (Jigglypuff, Marill, Gardevoir, etc), these too began to show magical fairy-like traits. Thus, professors in the Kalos region decided to recognize Fairy as a new type.
Kind of a lame explanation as I thought of it in about 3 minutes, but I guess it works. Or, you know, they could just not say anything. We know why Fairy exists, it's because GameFreak wanted to bring something new to the table. That's the explanation. Pokemon's not a plot driven game, so they don't really have to explain it in the universe of the game.
Official Something of Somewhere http://i.imgur.com/83ZkrSm.jpg
Maybe, since it's the Kalos region they are introduced in, perhaps it's the land itself that brings out the fairy type pokemon and their properties. The place is shaped like a star after all and looks pretty mysterious.