All we know so far about differences are 3 exclusives. It likely won't matter much unless you want those exclusives on your main run, and even then you can just trade.
Exclusive to X
>Clauncher>Swirlix>XerneasExclusive to Y
>Skrelp>Spritzee>YvetalHere on the X/Y site you can learn about all the other shit in the game as well.
http://www.pokemonxy.com/en-us/root/ 