Nightsky is a fantastic puzzle game, i highly recomend it.
Also, there's a game of the now defunct Imageepoch called Toushin Toshi Girl Gift RPG. Is a remake of the original (the original was a hentai game), and now is a RPG with heavy fan-service (+ 17, but to be honest, seran kagura games on 3DS are more heavy) . Despite that, its a good RPG with great monster and character design, but the people dissmiss the game because the original. Japan exclusive.
Kaitou Joker: Toki o Koeru Kaitou to Ushiwareta Houseki: The game is based on the manga of Kaitou Joker. Its not the best game on 3DS, but for a manga/anime adaptation, its pretty good and use some of the 3DS gimnicks like gyroscope and that kind of things. Its another japan exclusive.
Shingeki no Kyojin 2: Mirai no Zahyou, its the sequel to Attack on Titan Humanity in Chains. The game came out on the final years of the 3DS, and is a japan exclusive, so many people is unaware of the existance of the game (Also, the release was close to AOT 2 from Tecmo Koei, and that doesn't help at all. I have to admit that the first game of Spike Chunsoft was not good). It corrects most errors from the previous game, includes all the story missions from the first game, expand the wold mode letting you build your own Walls/fortress. It has more different titan transformations and more skills to customize, and add a new kind of weapons.
Another japan exclusive: Raishi - Konpeki no Shou, its a turn based strategy game.(Its also available on PS Vita)
... There's more"hidden gems" but most of them are japan exclusive..
