Seconding Picross 3D: Round 2. There's a ton of the best JRPGs of all time, like Bravely Default, Etrian Odyssey IV, and Shin Megami Tensei IV and SMTIV Apocalypse. Pocket Card Jockey is a masterpiece.

A Link Between Worlds is my favorite Zelda, the surprising open endedness is really refreshing. And Samus Returns debuts a lot of things people loved about Metroid Dread and is a great game on its own.

Rythem Heaven Megamix and Wario Ware Gold are compilation games for great series, but something is kind of lost taking them out of their original games. Megamix is maybe the one that's the most special in bringing everything together.

Rusty's Real Deal Baseball is completely nuts but I'm not sure if the experience is the same on a homebrew, as part of the game is haggling down the price of the DLC. Really good tho.

I love the 3DS