The only large difference between both games are the exclusive pokemon that you can get on either version, plus each of the version's legendary pokemon (the one in the cover of each respective game, Xerneas for X and Yveltal for Y).
Here's a list of each version exclusive pokemon: http://serebii.net/xy/exclusives.shtml
There's also some minor differences, such as some evolutionary items being exclusive to X or Y, but that doesn't usually affect your choice.
Personally I went with Y because of Yveltal.
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