Between these I had to go with Super Mario 3D World, because most of the list is dominated by games that focus on graphics and cinematography rather than interesting gameplay or anything that encourages problem solving and strategy.
Whereas I think SM3DW brought the best new ideas to the Mario series for a while (Though not as good a game as Galaxy, has better new ideas).
This was a pretty weak year for the sort of games I prefer, probably due to the transition period between gens. 2012 had XCOM, The Last Story, Growlanser IV, Legend of Heroes Trails in the Sky, Mass Effect 3, Tales of Graces, and so on, all of which I liked better than anything from 2013.
I might have to go with Tales of Xillia as my favorite game released in a generally meh year. Though I haven't played Dragon's Crown yet.
Like, Last of Us has a wonderful story, beautiful cinematography. It easily wins 'Best movie releases among games'. But the gameplay is boring and stealth executed really mediocrely. So the great story is like I'm eating shitcake with delicious frosting.
I think most gamers feel the reverse now, that the story/cinematography is more important than the gameplay. Most of this list is dominated by those kinds of games.
2014 is looking to be a little more exciting for non-cinematography oriented games. Persona 5 is definitely at the top of my list there, but Dark Souls 2 and Bravely Default come early in the year.