So looking at the titles of the new Generation 6 games, I believe that this series of games may have something to do with DNA. Part of the reason for this is because after reading a post where someone mentioned DNA, it hit me. In DNA, X and Y are chromeosones that are key parts of it. This theory may be true, but I'm not stating its 100% accurate. Plus we have Pokemon like Mewtwo, Deoxys, Genesect, and other prehistoric pokemon (by the way, I do not consider Mewtwo, Deoxys, and Genesect as legendary Pokemon).
Also look at the japanese logo for the games. Its got a DNA symbol in it.