Ishi-Sengoku-Den "Sadame". It's basically a 2D top down brawler style game with randomized loot drops a la Diablo, styled after Sengoku era Japan. Weird game, but a fun one for a unique Diablo like experience on 3DS.

Automaton Lung is fantastic. It came out right at the tail-end of the eShop's life.

Gotta Protectors is a great "2D Musou" game, Bloody Vampire is a fun Metroidvania style game with bump combat, Legend of Legacy is my favorite SaGa game (it's not a SaGa game) and The Starship Damrey is a short first-person horror adventure game.

That's all I could think of at the moment. All except Legend of Legacy are download-only games, so they are lost now.

I remember turn based strategy games finally clicking with me when I played Lord of magna. Idk how obscure that is though

Is ninjatown obscure enough?

Not sure if it’s really that obscure but Picross 3D round 2 is one of the games I have put the most time in to.

Not exclusively 3ds, as it's a ds game, but Okamiden. Underrated sequel to Okami, another underrated game.

Puyo Puyo Chronicle. It's exclusive to Japan, but Precise Museum made an English translation patch for it. It's an entry in the competitive puzzle game series Puyo Puyo, this time with a full blown JRPG attached to it. The story and levels are a bit simple so it can get a bit stale towards the end, but the gameplay is an interesting twist on the Puyo formula. Puyo Puyo has a bit of a learning curve to get started, but once you get over the initial hump, you'll be addicted.

Chronicle competes with 20th Anniversary for best game in the series. 20th Anniversary is also on 3DS, with its own English patch in the works. The original DS version of 20th is already patched if you don't want to wait.

Not sure if it counts as obscure but definitely not mentioned much.

Ever Oasis: single player town builder/adventure dungeon puzzle. It's like a mix between legend of Zelda and animal crossing but falls a little short on the town building. Still insanely fun though. Wish it had multiplayer