So, I looked up a list of games released this year (I always forget which games were released this year as opposed to last year).
As I've said, I mostly played 3DS games this year, with my favorite being Theatrhythm. I also really enjoyed Code of Princess (although I only played all the way through with Solange, I still need to work on leveling up the other characters), Resident Evil Revelations, Crashmo (Pushmo was one of my favorite 3DS games, and this is the sequel with new game mechanics), and of course, Kid Icarus. I'm still playing Virtue's Last Reward and Paper Mario.
For the Wii, I think the only games I bought this year were Rhythm Heaven Fever, and Kirby's Dream Collection. I also bought myself a Wii U but the only games I have so far are Nintendoland and NSMBU, so I can't really say much about either console this year.
I think my favorite home console game so far this year is The Walking Dead, but I still have a mess of games I have but haven't played yet including Mark of the Ninja and Dust: An Elysian Tail. Also, I really want to play Assassin's Creed 3, Dishonored, XCOM, Darksiders 2, etc.
So, I haven't played all the games I want to this year, so at the moment my favorite game of 2012 is Theatrhythm, but I'm sure that will change.