For Wii, my GOTY is The Legend of Zelda: Skyward Sword. Yes, I agree that there are problems with the pacing, occasional control snafus, and a lot of padding. I also agree that the story and characters are great even if some did not live up to their potential, most notably, Fi. Ultimately, I find the core gameplay of running across the land, solving puzzles, and fighting beasts throughout the dungeons so utterly engrossing that I feel justified calling this my overall Game of the Year.
For DS, my GOTY is Pokemon Black/White. The fact that the developers attempted to give the game a darker, more compelling narrative certainly helped, and the core gameplay of capturing and raising the hundreds of monsters to be as fun as ever.
For 3DS, my GOTY is Super Mario 3D Land. What else is there to say? The controls are great, with superb level design, and the overall package is just ripe with content.
On Wii VC, it's Chrono Trigger. Fantastic game, go play it. On 3DS VC, and this is probably on no one's list, but I picked Game & Watch Gallery. I went into it with modest expectations and found one of the most addicting and replayable games of this year. As for 3DS Downloads, I went with Freakyforms: Your Creations, Alive!. It's Nintendo-like to its core: simple to understand and get into, and can be very enjoyable to play. Not to mention it gets a few laughs out of me almost every time I play it.
Sure, there were some bumps, but overall, I'd say it was a good year for these platforms. Here's hoping next year is great as well.