You could go by the European literary perspective that Dragons and Fairies take. After all, Fairies in the traditional sense aren't just the cutesie little wood sprites.
Dragons in western lit are almost always take antagonistic roles as the big enemy opposing everything.
Fairies were sprites that did not serve a side and only spread malice to the good and the evil. Its very role, as seen here, is to disrupt.
It fits in with my theory that Game freak has been desperate to get the older fans off their back and did this as an ascended form of speculation. They've been doing a lot of fanservice lately, evident in the return of Charizard in the anime, butterfree's reappearance, Ash's evolving more, and a larger emphasis on returning Pokemon--games and anime-- back to their roots. The fairy was a rushed form of disruption only meant to crush dragons.
The TL;DR, It seems that mythological creatures are the only thing able to defeat other mythological creatures, a theme evident in a lot of children's entertainment. It was Jackie chan Adventures where Uncle always says "Magic must defeat Magic."
At the end of the day though, Dragons and fairies are in the same role that Psychic and dark Pokemon were in back in gen ii. It's to help balance all the types' rock-paper-scissors system a bit more. How much it actually has is yet to be seen.
The only source I really need is right here. Who else wants a piece of Uncle?