Travelling a lot, an waiting a lot, I spend a lot of time with my Nintendo hand held. In no particular order:
Smash Bros is probably obvious. You're not really missing anything if your 3ds doesn't support amiibos. Mine does being a new nintendo 3ds xl. I have amiibos for the hell of it more than anything.
Tomodachi Life is a neat little diversion.
Scribblenauts in general is nice, though the game seems to lack the power to let you make your own maxwell for some reason.
A little more in the family of intellectual stimulation is Art Academy: First Semester which is about as clear cut of a title you could want.
Brain Age express is some good mental exercise.
Being free unless you want to spend money, pokemon Shuffle, and Pokemon Rumble World are ok.
Pokemon Battle Trozei is not too bad.
Pokemon OR/AS, and Y/Z are hard to go wrong with, though pokemon Z is coming out. t depends on if you'd rather wait on it.
Project X zone is a bit of a slog with an almost guaranteed 2 stage battle, but all the wonderful characters coming together and the craziness of seeing 5 of them wail on an enemy at the same time is nice, IMO.
Fire Emblem Awakening deserves mention. It's a great series in general.
Senran Kagura Burst, and Senran Kagura Burst 2: Deep Crimson both deserve some attention, imo. Great brawlers.
Samurai Warriors Chronicles, and Samurai Warriors Chronicles 3 are some I recommend.
Lego Batman 3 is a fun game.
Rune Factory 4 is a solid top down RPG with a lot of heart.
Fantasy Life is not bat at all.
Shantae and the pirate's curse is an awesome platformer.
Out of left field is Style Savvy: Trendsetters! What ever you might think of putting together outfits, there's a strong satisfaction in pleasing customers.
Starship Defense is a neat tower defense game on the cheap.
Are you a fan of Battleship? Radar Mission takes the game to new areas.
Kersploosh is a neat game where you take up the role of an object thrown down a well, and have to dodge obstacles to see the bottom of the well.
Demon Box King reminds me of Makai Kingdom plot/characterwise, but it's a lane combat game where you send units along lanes to do combat with enemy units.
Don't be afraid to use the backwards compatibility. Final Fantasy tactics a2, Sims pets, Pokemon Conquest (though having to go through the side stories to get to a more free play sort of thing sucks.), Civilizations, etc. can make for an interesting time.
What I wish i could do is recommend a game in the style of Romance of the Three Kingdoms, but what they released was Japan only. :/
Hit up every Demo you can. You never know!
Also, look up how to format large Micro SD cards for your 3ds! The space will come in handy, and do it before you invest too much in your current one!