In my opinion, I think the next two Pokemon have a major role in the history of Pokémon.
First, Yveltal has some clues in his name, like all other Pokemon. Its name comes from the term "Yvel" which means "evil". Due to its relatively aggressive forms (spicy), its color is both aggressive red and black colors, does not bode positive!
Second, Xerneas is a deer, a creature of the wood is therefore akin to nature. Given the highly colorful and sleek this pokémon, my instinct tells me that I can trust this pokemon so graceful and beautiful!
In conclusion, I think it will be between a hero (you) and these two Pokemon that will be used for evil. Due to their power, as usual. Seen every legendary pokemon are used because of their powers, I think it will be between two powers of the two legendary pokemon:
The order / creation / nature (Xerneas)
Disorder / destruction / chaos (Yveltal)
What do you think?