I’ve been reluctant to downplay a specific year so far, but 2012 is pretty rough by my personal standards. The absence of Xenoblade really hurts it.
My pick is Zero Escape: Virtue's Last Reward. I’m not typically a visual novel guy, but Zero Escape manages the transcend the genre with challenging puzzle-solving gameplay, memorable characters, and Rashomon-style storytelling.
Second place would probably be Wipeout 2048. I loved all the modes, the blistering pace, the track designs, and the clean visuals.
2012 was a good year for Vita.
Mark of the a Ninja also deserves a mention. Just a brilliant stealth action game.