Okay, here is my top ten (my personal opinion and taste!)
1. Fantasy Life - really cute game, lots to explore and do (picking up 12 different lifes like fisher, paladin, alchemist, woodcutter, miner etc- You can either play only one life or chose them all!). That game is beyond charming, I enjoyed the story and the quests. the characters...this game is one of the most underrated 3DS games imo!
2. Rune Factory 4 - similars reasons like fantasy life. I like the rpg/ farming cross over. I'm biased bc I love Harvest Moon / Story of Seasons/ the Rune Factory franchise
3. Ever Oasis - gives me slight TLOZ vibes. Also, great story and amazing soundtrack!
4. Pok?mon Sun/ Moon/ UltraSun/ UltraMoon- love the tropical setting but not a fan of the too linear gameplay
5. ACNL - for obvious reasons!
6. TLOZ- Link between world- Idk, I just enjoyed playing it a lot I guess!
7. Ace Attorney: Dual Destinies- a detective game. lots to read but GREAT dialogues and cool characters. I love the entire series and I prefer Dual Destinies over Spirit of Justice.
8. Story of seasons- I love both games (there are 2 currently). There is so much to do and I'm a sucker for cheesy dating sims xD
9. Yokai-Watch!! Both games again. I love its whackiness and how much japanese culture its showing.
10. Kirby Triple Deluxe - So much to discover and a great platformer