1- Animal Crossing New Leaf
2- Super Mario Maker for Nintendo 3DS (I'm know the Wii U version is better, but I've never had a Wii U...)
3- Luigi's Mansion: Dark Moon
1. Fire Emblem Fates + Awakening
2. Pokemon / ACNL
it's funny considering I only bought the 3ds for Pokemon XY to begin with, but bought Fire Emblem first and it completely enthralled me more than anything ;'))
Pokemon Omega Ruby & Alpha Sapphire
While I greatly prefer X & Y and Sun & Moon for having trainer customization and more interesting regions, Omega Ruby & Alpha Sapphire are a happy medium. They feature more Mega Evolutions than were in X & Y and a number of those aren't even available in Sun & Moon. Additionally, they felt fulfilling enough and even though there's not a whole lot of postgame, all of those legendaries helped me fill out my National Pokedex and I even managed to soft reset for and capture a shiny Kyurem after getting the Shiny Charm. They include the Super Training feature that I love and which wasn't included in Sun & Moon, and the fact that the Elite Four's Pokemon increase in level in rematches unlike in X & Y made levelling team members to 100 very simple and easy.
Animal Crossing: New Leaf
Considering this is an Animal Crossing forum and the fact that I don't have a wide variety of 3DS titles, it's unsurprising that it's one of my favorites on the system. There is a ton of content that has kept me busy and entertained on and off for years now. Definitely my favorite installment in the series, and whatever next main series game comes out will have a lot to live up to if it wants to compete.
Fire Emblem Awakening
While I absolutely cannot find enjoyment in this game and greatly dislike where the series has been for the past nearly 5 years since its initial Japanese release, it is a fact that the series would be dead without it. I wouldn't mind the series dying back then as it currently stands, but it made Fire Emblem Echoes: Shadows of Valentia possible and depending on how they handle remaking that, I may at least owe this game a debt of gratitude.
If Fire Emblem Echoes: Shadows of Valentia is good, it will replace Awakening in a heartbeat considering my disdain for Awakening. If they flub it up somehow, I'd put Kid Icarus Uprising in Awakening's place here. I didn't even play Kid Icarus Uprising, but it has received a lot of praise and one of my friends has raved about it in the past so I'd give it a nod here.