If I haven't already said it enough, Virtue's Last Reward is one I'd recommend, it easily places first in my favorite games on the 3DS (and of the eighth generation, so far). The game lasted me about 40 hours, but that can vary from person to person depending on how you deal with the puzzles. The story for the game is unparalleled, so I definitely recommend buying it.
Fire Emblem: Awakening comes in a close second, and its up there with Genealogy of the Holy War as my favorite Fire Emblem titles. It's a game that's as long as you make it out to be, and there's a lot of replay value (though not in the conventional sense), as well as a good story and a surprisingly strong cast of characters. I'd definitely recommend it, even if you don't like strategy games.
Kid Icarus: Uprising is also a great and very unique title, and I think of the three games I've listed so far it has the most overall appeal. It has clever dialog, plenty of references, and fun gameplay. But as Spinosaurus said, the controls can be a little painful, but once you get past that you'll have a lot of fun.
If you're looking for eShop titles, I'd recommend Harmoknight, a Rhythm game made by the creators of pokemon, that is pretty short but has more to offer upon completion.
Crimson Shroud, a Guild 01 titles, is an RPG in the style of D&D, and as complex as it is, it features a lot of decision making with immediate pros and cons. It's certainly an interesting title that makes a lot of interesting choices in its development, and its certainly worth looking into if you like Turn-Based or Tabletop RPGs.
Liberation Maiden is another Guild 01 title worth looking into. It's a Shooter much in the style of an Action Game. It's missions offer variety, and the missions often have side-missions, making each more varied than the last.
