These aren’t all games I’d declare fantastic or even pretty good, but here are a few that I feel are noteworthy:
Legend of Legacy: this is one of the better games from FuRyu, a publisher whose MO is hiring a few big-name personnel from established popular RPG series and having them make ripoffs of their old games with subcontracted studios—in this case, they got a few ex-SaGa people (plus Masato Kato) to lead a totally-not-SaGa game, and while it’s not necessarily all that SaGa-y outside of the combat, and it’s not-so-secretly a dungeon crawler rather than a traditional JRPG, I thought it was fun enough. (Alliance Alive, which recently saw a HD remaster on various platforms, is a sequel to this game, but with a more conventional structure and a story by Suikoden series writer Yoshitaka Murayama.)
Shinobi: this was an early 3DS game that was written off for being a poor showcase of the graphical capabilities of the 3DS during a time where pessimism around 3DS was at an all-time high, but it’s a very credible hardcore action game on a system with few alternatives (but emulate it rather than actually play it on 3DS).
Mario Party Star Rush: this game’s novel for the main mode being completely unlike the other games, before and since—the boards are grid-based, with simultaneous rolling/moving for all players, and you play as coloured toads rather than Mario & co. (who are instead recruitable/stealable allies). I’ve played so little of it with other people that I can’t evaluate how fun it truly is, and the game itself has other issues (like relatively few minigames spread across several secondary modes that aren’t fun) but it might be worth checking out for the sole fact that it’ll probably be a one-off.
Style Savvy/New Style Boutique: Nintendo put out three of these on 3DS and the first one, subtitled Trendsetters in NA, is probably the one to get if you explicitly want to experience the retail business sim elements, as the others veer harder into general dress-up or idol gimmicks or what have you. (These games were made by syn Sophia, formerly AKI Corporation, as part of their somewhat abrupt shift from wrestling/combat games to galge.)
Harvest Moon: Skytree Village: this is the third Harvest Moon game produced directly by Natsume USA (ie it has nothing to do with the original Japanese series, Bokujou Monogatari) and of all the Natsume USA-produced games, I think it’s the only one worth playing—the 3DS games went in a Minecraft-esque cubic 3D direction with terraforming and so on, with a lot of complexities to crop cultivation, so if you want a farming game (and specifically a farming game, not a relationship game or a broader “hangout” game, because Natsume sucks at all that stuff) that’s distinct from BokuMono, Stardew, etc I think this game offers a genuine alternative. (After this one, they went back to 2D and stayed there, and while I hear they’re no longer terrible at 2D like they were in the beginning, AFAIK they don’t even attempt anything novel and most of them recycle the same characters.)
Japan got loads of games that never got localised, obviously… the second Etrian Mystery Dungeon/Sekaiji to Fushigi is one of the higher-profile ones, off the top of my head. This was also the era of big JP publishers trying and failing at big cross-media kids’ IP, so there are relatively high-production games like Gaist Crusher (which was also Treasure’s last game), Hero Bank and Gyrozetter that you might want to look into.