I know this thread is oldish, but I missed it and wanted to post mine.
The sad answer for my best 2012 3DS game, excluding ports, is... Kid Icarus: Uprising. I know it's cliche and people are probably rolling their eyes, but it's the truth. The thing is, I didn't get my 3DS until 2012 (January), and I never owned any of the DS systems, so my 3DS gaming has consisted mostly of 2011 3DS games, and tons of DS games. The only 2012 retail 3DS game I played at all besides Kid Icarus was Resident Evil: Revelations, which I haven't played enough to really make a judgment of, and demos of MGS3D and KH
DD, neither of which I cared for.
That said, there were tons of great eShop titles (again, excluding ports) that I liked... Mutant Mudds, Fractured Soul, Liberation Maiden, all come to mind. And I can't remember if they came out in 2012 or not, but Sakura Samurai and Mighty Switch Force were really great, too.