Games that loads have said already; SMT IV Bravely Default, Bravely Second etc.
One note about Shin Megami Tensei IV is that there is two "versions"; The base game and "Apocalypse Edition". These are not the same game, but different routes and Apocalypse is made for people who played the first one through. SMT Vengeance actually does the same idea, but packs both routes into the new title, while 3DS might had constraints about that or Atlus had money making ideas in their head. If you are interested in the game, do note that Apocalypse is not same as "Royal" as the experience will be substantially different from the main game before it.
I feel somewhat different from scrolling my actual 3D through to remember some titles I really remember. I cannot tell how fun street pass was as a thing when it was a thing, and nothing can quite replicate that feature and big N-word was truly dead inside when they did not think doing it again with switch.
Zelda: Link Between Worlds, To some last good 2D zelda experience, even if it is in 3D, and uses that for it's gameplay gimmicks. Absolutely nice Zelda adventure that for long time was last of it's kind as re-releases and HD editions were only things added. Have not heard does the new game with actual Zelda hold a candle to this one.
Virtue's Last Reward, (& 999) Though this is not a recommendation to play it on 3DS or an 3DS emulator, there is also generally superior Vita version as well as collection that has versions on PC and consoles, vita too (so vita has two releases of VLR and that is fun). To me though, VLR is a special game for 3DS as it was first one I bought for it, and after the end was glad I got the console and the game. There is a nasty 3DS exclusive bug though, where one should avoid saving in certain puzzle rooms or scenes and if you do, you need to wipe your save and start clean over. I do use this though to implore and recommend also Nine Hours, Nine Persons, Nine Doors or 999 and implore anyone with a 3DS or DS to play this game for the first time with that version. Maybe even emulator, but first experience with the new version, even if it has excellent voice acting at least in Japanese, is very much a diminished one.
Professor Layton Vs. Phoenix Wright. This one is somewhat forgotten but a great ride and possible cross introduction point for fans of one series into the other. This one also has not had any release on other platforms and remains true exclusive where the Wright games have not. There is also 3DS layton games few having versions for mobile but not all of them. Fun note is that Wright sections have a unique gameplay mechanic from the "Great Ace Attorney" series that did not come outside Japan for longest time, making it for long the only game with the mechanic for western players.
