With the announcement of Mewtwo being the secret Movie 16 star, it is only natural to wonder what this may mean for the games. Previous generations were heavily promoted by the movies leading up to their release, but in this case the stars of the main movie (as opposed to the short) aren't new species. While Genesect was due for a movie role, Mewtwo already has a movie and a special (technically two specials) under its belt. Why would the Pokémon Company want the movie to be focused on Mewtwo unless it were relevant to the upcoming games?
Mewtwo's name has already been brought up in the context of X and Y due to the probable Genetics theme. But some fans seem to have dismissed that theory simply on the basis of Mewtwo (and Mew and Deoxys for that matter) being old news. But if Mewtwo is good enough for the movie, why would it seem out of place in the games? If anything, there should be some old legendaries in the games so that Game Freak don't have to go overboard with new legendaries just to fill some quota of sidequests. A lot of existing legendaries have untapped potential story-wise, and Mewtwo and Mew are among the prime examples as I explained here.
While a movie-related download could work, Mewtwo has already been distributed in the current generation. It would be far better if it were catchable in X and Y and had some connection to the main story. I am particularly interested in seeing Mr. Fuji again, who is by far one of the most enigmatic characters in the series. Not only could Mewtwo's real origin story be finally told in full, but I could also see a connection to the new bonding feature. Dr. Fuji may have created Mewtwo solely for battling, but Mr. Fuji clearly doesn't see Pokémon that way. No doubt Mr. Fuji would want Mewtwo to finally find a trainer that could manage to open its heart and earn its trust.
On another note, the theory about Mew being the ancestor of (most) Pokémon could finally be touched upon. I wouldn't be surprised if Mew were connected to Xerneas and Yveltal.