(Please don’t say Pokémon)

Mystery Dungeon: Explorers of Sky

The Legendary Starfy, Super Princess Peach, Magician's Quest: Mysterious Times, Fossil Fighters, Legend of Zelda: Spirit Tracks, Tomodachi Life, Harvest Moon: Grand Bazaar and Tale of Two Towns (separate games), Kirby Superstar Ultra. I know you said no Pokemon but…. all 3 Pokemon ranger games, they were and still are my shit, I hope they make one for the switch at some point…

Fun fact, I literally pulled out all my DS games to make this post lol, I omitted quite a few.

ds:

• kirby canvas curse, super star ultra (obligatory to mention, these were my childhood)
• mega man star force 1 and 2 (successor to the gba battle network series)
• all the castlevania games (theyre all pretty good)
• dragon quest joker 1 and 2 (like pokemon but dragon quest)
• scribblenauts and super scribblenauts (weird puzzle games)
• custom robo (mech game for kids, but you can make your own little toy mech which is pretty cool)

3ds:

• kirby triple deluxe and planet robobot (also obligatory)
• shin megami tensei iv + apocalypse (really good and really hard rpgs)
• all the etrian odyssey games (also really good and hard rpgs)
• professor layton miracle mask and azran legacy (british)
• culdcept revolt (personal fav, mix between magic the gathering and monopoly)
• little battlers experience (another mech game for kids)

My favourite 3/DS games where the Ace Attorney games but they are now available on Windows (also virtually all platforms).

It's gotta be Style Savvy: Styling Star

Ghost Trick Phantom Detective is an amazing game. Just play it.

Got oddly hooked Might and Magic: Clash of Heroes too.

For the NDS I recommend Radiant Historia. It has an excellent story and the same composer as the Mario RPG games. It's as "hidden gem" as it gets

Yo-kai watch 2: psychic specters

I was more of an NDS kid because I was already older by the time the 3DS came out and I loved obviously Nintendogs and Animal Crossing, but also Another Code, Harvest Moon and Rune Factory, the Mario RPG games, and of course my absolute favorite Lost in Blue. That game was the first real survival game to ever exist and I remember spending hours just taking care of my bars over actually progressing the story lol (also because I figured the story was going in a sci-fi direction I didn't care for and that game was seriously hard af).

Of course that's just the games I grew up with, later on I was able to play Ghost Trick, Professor Layton, Phoenix Wright and the two Zelda games still on the NDS. Also love Theresia and touch Detective, which I think count as hidden gems. I especially recommend Theresia. But like I said I played those years later so I don't count them with the bulk of what I played as an actual kid when those games came out.

For DS Games Rhythm Heaven is really fun, it's basically a collection of rhythm mini-games. Another good one is Mystery Dungeon: Shiren the Wanderer, from the same series as Pokemon Mystery Dungeon but with less focus on the story and more traditional roguelike mechanics. For 3DS, someone already said it but Shin Megami Tensei IV is a fantastic RPG.

Planet puzzle league, a simple match 3 carried by its soundtrack, including the 7/4 banger "Enigmatology".

I really liked the Devil Survivor games. Tactical strategy RPG in the Shin Megami Tensei series. Incidentally one of my favourite big franchises.

They re-released the first game on the 3DS and it's a solid port. Speaking of SMT games, SMT: Strange Journey is another good one. It has that very classic dungeon-exploring RPG vibe though, which isn't for everyone. Think Etrian Odyssey or the old Wizardry games.

For the DS, some that come to mind which haven't yet been mentioned (and which aren't available elsewhere):

Solatorobo, Dragon Quest Heroes: Rocket Slime, Monster Racers, Final Fantasy Fables: Chocobo's Dungeon (available on PC but they removed the pop-up card game, heresy) 😖

As for some other DS games that honestly probably have better alternatives, but that I also have fond memories of-

Phantasy Star Zero (a big part of my childhood, playing multi- all pirated of course- with my sibs), Ragnarok DS (Ragnarok Online but DS), Atelier Annie, Kingdom Hearts 358/2 Days

For the 3DS:

Ever Oasis, Shin Megami Tensei: Strange Journey Redux (updated port of the DS game, very similar to Etrian Odyssey mentioned in this thread- and great), Shin Megami Tensei: Devil Survivor Overclocked and Devil Survivor 2 (SMT formula, but with grid-based tactics), 7th Dragon III

(edit) also forgot-

For the DS: Dragon Quest IX, Infinite Space, the Tales games that are on the DS (they have fanmade English patches, those that aren't released outside Japan...), Sands of Destruction.

I did recently too! It's crazy how far the homebrew scene has come.

One I never see mentioned: Alice in Wonderland on DS. You'd think it was based on the awful 2009 tim burton movie, but it's actually a completely original puzzle platformer with great design and a fantastic art style.

Edit: also suggest you download MGBA for it because that's the only system afaik that can emulate the gyroscope GBA games like Yoshi Topsy Turvy and Warioware twisted.

PokeDigimon World Redigitalize on the 3ds, although there isn't an official translation, the fan translation is really good.