Uh, very difficult to choose only one, there are several that I like dearly: Bravely Default, Heroes of Ruin, Fantasy life... but I guess it would be Ocarina of Time/Majora's Mask duo
It's a toss-up between Pokemon X, Y, Omega Ruby, and Alpha Sapphire. X & Y and ORAS each have positives and negatives so they just kinda balance out in my mind.
Dammit I love so much games! everbody likes RPGs now?
Nintendo Presents: New Style Boutique 2
Tomodachi Life
Hatsune Miku: Project Mirai DX
Animal Crossing: Happy Home Designer
Yo-Kai Watch (waiting to buy full game :~: )
Super Smash Bros. for Nintendo 3DS
-Really enjoyable, but I have grown too used to Wii U's controls as it allows me to use a GameCube controller
Mario Kart 7
-Possibly the best handheld Mario Kart, I however do not play it much as I completed the game and Online doesn't offer much to me anymore.
Luigi's Mansion: Dark Moon/Luigi's Mansion 2
-Very great game that uses the 3D feature well on Nintendo 3DS. I feel it could have been better without the gyro controls though...
Pilotwings Resort
-Great successor to the Pilotwings games and controls quite well compared to the other games. I wouldn't recommend using 3D on this game though as it is very harsh on the eyes.
Fire Emblem: Awakening
-Great continuation of the Fire Emblem series and my first game in the franchise. Haven't progressed far into the game though...