To tell you the truth, i cant decide without knowing if i can, or cannot use downloadable games. If i can it would easily be pokemon red. If i can't then its between pokemon ORAS or batman blackgate. I think in the end i would choose ORAS though.
For me it would definitely be:
Luigi's Mansion: Dark Moon. I know it's not as good as its predecessor and that's not a 3DS game.
I love every bit of Luigi's Mansion: Dark Moon. Not to mention it looks absolutely beautiful in 3D! The gameplay experience also is a lot better with 3D effects. This game is meant to be played with the New 3DS!
Well I cannot go with any Pokemon games here, because I have to go with 3D Land as well. I was overall pretty unimpressed when it comes to the 3DS, so I would just like to think that at least they got the basics down. As long as the Mario game is good, I can say that I got what I expected from a Nintendo system. I would have liked a little more, but this was a fun game.
I would probably say my favorite 3DS game is a tie between Fire Emblem Fates and Animal Crossing New Leaf, I have played these games since they came out and I still do, it's hard to decided which one of these two is my ABSOLUTE MOST FAVORITE but it's definitely between these two games.