Not that it matters to anyone with cfw, but as LRG's release of Axiom Verge for Wii U showed, any 3ds title they release physicaly will be region locked.
I am also working on a 3DS game library, but I am trying to get everything digitally. Games that I have that you did not list are
*Minecraft
*Kirby's extra epic yarn
*Tomodachi Life
*Terraria
*NES Remix
*Bowsers inside story remake
*Art of Balance
*Pokemon Shuffle
*Pokemon Rumble World and Pokemon Rumble Blast
*Sonic Generations
*Smilebasic and Pettit Computer (make your own games with a modified basic language)
*Puzzles and Dragons Z+Super Mario Edition
*Super Scribble Nauts Unlimited
Most of these are not available anymore physically (besides Kirby's extra epic yarn and bowsers inside story remake. I'm not sure about Minecraft though.) the only digital exclusive game there is on that list is Pokémon Shuffle.
Have you tried Attack on Titan: Humanity in Chains and My Hero Academia? They're both based off an anime but the games are fine for me. Harvest moons: Tale of two towns is a DS game but it's also available for the 3ds, My favorite from the series because you get to move between two towns. You should also try Need for Speed: No limits if you like racing games. As for my Personal Favorite it would be Stella Glow.
I'm also looking for recommendations, preferably RPG's, Visual Novels(except the ace attorney or professor Layton series) or Story driven games
I do have harvest moon and my favorite is the normal harvest moon ds
As for rpgs and visual novels it depends what you are looking for i can reccomend a few titles some are for the ds
-Last Window(DS)
-Hotel Dusk Room 215 (DS) if you love visual novels i cant reccomend this two games enough
-999 9hours 9doors 9 persons (DS) quite an awesome visual novel and puzzle game
-Virtues Last Reward (3DS) a sequel or a pre sequel to 999 definetly worth it
-all Fire Emblem series (you probably knew about those)
-Radiant historia (DS&3DS) good rpg
-Golden Sun (DS) needs no explaining
-Chronno Trigger (DS) snes port if you love rpgs there is not a reason of not getting it
-Fantasy Life (3DS) check YouTube for reviews i cant really explain how awesome this game is
-Ever Oasis (3DS) simillar to fantasy life
Hit me up if you need other suggestions i just did a few from a lot
I just got Radiant Historia 2 days ago, Haven't played it yet though. As for Fantasy Life, 999, and Virtues Last reward, I've heard of them but I'm still deciding though I guess I'll be getting them since many people recommend it. I'll be checking out Last Window, and Hotel Dusk Room 215. Thanks for these recommendations. I hope they give me a good play