My vote goes to The Last of Us here, followed closely The Legend of Heroes: Trails of Cold Steel whose original Japanese release date was in 2013, but there are quite a few other games I enjoyed as well from 2013. Papers, Please, the Tomb Raider reboot, The Stanley Parable, Rogue Legacy, Brothers: A Tale of Two Sons, and Guacamelee! were all great in various ways, just not quite the best of the year.