Golden Sun is worth checking out. Also Zelda OOT/MM/Link Between Worlds, Fantasy Life, Animal Crossing New Leaf, Bravely Default and Bravely Second, Tales of the Abyss are all ones that come to mind. Plus Metroid: Samus Returns if the RPG-esque elements of metroidvania are enough for you.
Final Fantasy; there are both mainline remakes/remasters but also FF Tactics titles. Fire Emblem also had titles on the system. Then there are Rune Factory and Story of Seasons (Harvest Moon). Pokemon and also the Yokai Watch games, and Xenoblade Chronicles (New 3DS exclusive, albeit a Wii port). Luigi's Mansion 2 was also a 3DS exclusive!
Honestly there were some absolutely cracking games on the 3DS! I still keep mine in the car; albeit given the world I don't play it anywhere near as much as I used to
Realistically, just jump onto metacritic and look at the user scores. There is a rather large library with high user and metacritic scores; the library had some real gems
Edit: I always forget Ever Oasis, but that always gets good feedback from actual owners, its one I missed.