The major difference which exist in Pokemon X and Y is in their Legendary Pokemons and Mega Evolved Pokemons.
Type : Fairy
Ability : Fairy Aura
In Pokemon Y, the Legendary Pokemon is "Yvelta".(Destruction Pokemon)
Type : Flying/Dark
Ability : Dark Aura
The Mega Evolution of Mewto and Charizard are totally different in Pokemon X and Y.
Mega Charizard X is Dragon / Fire type having the special ability of tough claws, while Mega Chaizrd Y is Flying / Fire type with a special ability "Drought" which increases its fire type abilities.
In Pokemon X Mega Mewto is Psychic / Fighting Type and its special ability is "Steadfast", while in Pokemon Y Mega Mewto gets the "Insomnia" ability which doesn't allow him to fall asleep.
List of Pokemon which are exclusive in X and Y are
|Exclusive Pokemon X||Exclusive Pokemon Y|
Again, which one you should buy? It has been found that the majority of the people bought Pokemon X, but it does not matter. I personally recommended my friend to buy Pokemon Y (It's better to be unique).