Virtue's Last Reward if you like graphic novels with puzzles
SMT series in addition to SMT IV also has Devil Survivor Overclocked and Devil Summoner Soul Hackers
Conception II... which is a literal dating sim mixed with jrpg dungeon crawling
Crimson Shroud is an incredibly old-school style game with damage determined by actual dice rolls and in a DnD setting

Bit. trip saga - Got it for $5 when it went on sale on the eshop. Runner 1 is worth that alone.
Rhythm King - Like Rhythm heaven/Elite Beat Agents/ Cing games? This game is a nice new IP
TheateRhythm - Like Elite Beat Agents? This is that with final fantasy songs. A crap ton better than the ios port.
Tappingo - a cool picross inspired game that is amazing. Only like $2-3 bucks on the eshop as well.
Ikachan - super short but makes great use of the 3D and is really fun. Made by Pixel
Liberation Maiden - Like speedrunning/ replaying fun games? this game is pretty awesome for that.
Mutant mudds - a fun platformer with great 3D use.
Ghost Recon: Shadow Wars - Like X-com/ Fire Emblem? This was the only good game to play on launch and its great.

A bunch of great games with variety of genres as well. Hope this helps dude