Another Legendary you can catch in the Kalos region is Mewtwo, who is found in that small cave within the Pokémon Village, after you have entered the Hall of Fame.
Make sure you prepare before heading out! Mewtwo has an extremely low catch rate (like most Legendaries), but it also knows Recover, making it an absolute pain to catch. In fact, if you are looking for a Legendary to use your Master Ball on, Mewtwo is not a bad option.
If not, make sure you have plenty of Dusk Balls and Timer Balls, with Ultra Balls being alright too. Having something that knows False Swipe won't be as effective here, at least not until Mewtwo runs out of PP for Recover, but having something that can paralyze it or put it to sleep may help immensely. You can also try using Taunt, though that will only last a few turns. Either way, be sure your team is strong enough to put up with Mewtwo's powerful moves, since it's very high leveled.
Lastly, note that you'll need something with Surf in order to reach Mewtwo.
To get there, you'll have to go to Snowbelle City and navigate through the Winding Woods again, but it isn't that complicated. From the entrance, go south (past the Moss Rock), then west, then north (past the Twins), then west of the Fairy Tale Girl, then south at the fork. Pass the large tree, and keep following the path south.
You'll see the cave, which previously had a man blocking it, is now accessible. Surf across the water to the west to reach it.
Enter the cave, known as the Unknown Dungeon, and you'll see Mewtwo, just standing there. Definitely save your game before speaking to it (in case something goes wrong, or you're resetting for a good nature/IVs).
|Legendary Pokémon: Mewtwo|
|Mewtwo||Psychc||70||Psychic, Aura Sphere, Recover, Barrier|
Once you manage to catch it, you will obtain a Mega Stone depending on your version. In Pokémon X, you'll get the Mewtwonite X, and in Pokémon Y, you'll receive the Mewtwonite Y.