Unlike some past Pokemon games, the differences between the versions are marginal. The main thing and really the only significant difference is in the Pokemon you can get.
-X gets the Mega Stone for Mega Charizard X while Y gets the Mega Stone for Mega Charizard Y. If you don't choose Charmander, this is of no importance. If you do intend to choose Charizard, then I would argue that Mega Charizard Y is the better Pokemon, as it has instant weather. While weather was nerfed, it still makes Charizard a difficult foe to handle, since it gets use of Solarbeam and more powerful Fire type attacks.
-X gets Starmie, Y gets Cloyster. While they serve different roles, Starmie is just a more important Pokemon than Cloyster is. Cloyster is arguably outclassed in terms of spinning and hazard laying, and its main draw is in Shell Smashing, which cannot always be used reliably. Starmie is just a great Pokemon with great speed, decent defenses, and a solid offense. Starmie is one of the best spinners in the game, and is always a great Pokemon to have on a team.
-X gets Pinsir, Y gets Heracross. Heracross is far better than Pinsir. No contest there.
-X gets Mega Mewtwo X, Y gets Mega Mewtwo Y. Both are powerful Pokemon, but my use of Mega Mewtwo Y has led me to call it one of the most dangerous Pokemon in the Uber tier. Mega Mewtwo Y is going to be the better option, thanks to higher speed and access to higher power STAB.
-X gets Houndoom, Y gets Manectric. Houndoom is the better Pokemon, as its ability to switch in on a multitude of Pokemon is incredibly helpful. Sucker Punch, Pursuit, and Flash Fire are a bit too good to pass up over Manectric's meh stats.
-X gets Mightyena, Y gets Liepard. Liepard is the better Pokemon, as it is much better in its support/annoyer role than Mightyena is as a Physical attacker.
-X gets Aggron, Y gets Tyranitar. Tyranitar is a metagame defining force, a driving Pokemon behind Sand teams, and a surprisingly great Special waller, in addition to its role as a Psychic/Ghost killer. Aggron is just a decently bulky Pokemon.
-X gets Cradily and Armaldo, Y gets Omastar and Kabutops. Omastar and Kabutops all the way. Cradily is a decent wall, but it isn't that useful, and Armaldo is just plain outclassed by Kabutops. Omastar is also a solid Shell Smasher.
-X gets Sawk, Y gets Throh. Althought the Storm Throw boost is nice, I'm going to have to give the win to Sawk, who is a defining force in the NU metagame.
-X gets Slurpuff, Y gets Aromatisse. Slurpuff. Aromatisse is useless, and outclassed as a supporter by Slurpuff. Slurpuff also makes a rather nice Belly Drummer.
-X gets Clawitzer, Y gets Dragalge. Dragalge wins this one, as its great defensive type, powerful Dragon and Poison STAB, and bulk allow it to be a very threatening foe. One of the closer match-ups though.
-X gets Xerneas, Y gets Yveltal. Xerneas is arguably the most powerful Uber right now. Fairy typing is just really good in a tier of Dragons. Yveltal is solid for dealing with Mewtwo, but Xerneas just sweeps entire teams with Geomancy.
X wins: Starmie, Houndoom, Sawk, Slurpuff, Xerneas
Y wins: Mega Charizard Y, Omastar, Kabutops, Mega Mewtwo Y, Heracross, Tyranitar, Liepard, Dragalge
Overall, I would say Y has more Pokemon who are important to their respective metagames. However, X does have Xerneas, who is basically one of the best Pokemon ever. If you have a particular favorites among the Pokemon, go with the version that has that Pokemon.
Overall, I would suggest Y.