if you have any other system that's capable of playing MGS3, I'd choose that system over the 3DS port. It was impressive for when it came out, but that 15 fps really killed the enjoyment for me. IIRC there's a demo on the eshop you can check out to see for yourself.
now to answer your question...
Fantasy Life
Rune Factory 4 (Probably not worth it as much if you cop Fantasy Life)
any of the Picross e games; e1, e2, etc.
Pocket Card Jockey is made by Gamefreak. It doesn't nearly enough love even when bringing up 1st/2nd party Nintendo games, so I'm adding that here. Most bang for my buck out of any 3DS game.
theatrhythm final fantasy is the best rhythm game for the system IMO. Lovely selection of songs from all the FF games, plenty of DLC too!
I forgot that the Bit.Trip saga also released on 3DS, that's also a phenomenal collection of rhythm games. The original Bit.Trip beat in particular is worth the purchase alone.
Monster Hunter 4U had my favorite single player out of all the 3DS monster hunter games. Idk if the online component is still active, but even then that's at least 100 hours of content for single player alone.
Outrun 3D is gorgeous. All of Sega's 3D classics are lovely, but this one's my fav.
Atlus's 3DS run was stellar. I def recommend you check out at least one entry from the 3DS Etrian Odyssey and Shin Megami Tensei games. I've only played Etrian Odyssey IV and SMT IV, which from my understanding aren't the best ones available on the system. You may want to do some more research for which one is right for you. With that in mind, I do not recommend Etrian Odyssey Mystery Dungeon. Too unfair for my taste. Shame there isn't a Shiren the Wanderer game...
Capcom's 3DS run was also fantastic. Monster Hunter was the cream of the crop, though.
BRAVELY DEFAULT IS THE BEST DAMN JRPG ON THE SYSTEM. Well I only played the first one. Apparently the 2nd is much better... so maybe that's the best damn JRPG on the system.
The Ace Attorney series is great. IDR if there were any 3DS exclusives in the series that made it west, but the rereleased collection of the GBA/DS ones is still worth checking out.
imo Shovel Knight looks and plays the best on the 3DS. I've played the game on PC, Vita, and Switch as well. The small screen really does wonders for the 8-bit aesthetic. This is another game that takes great advantage of the 3D feature.
Gunman Clive was a cute indie platformer. Sepia-toned cowboy vibes.
Dragon Quest VII and VIII both had admirable ports to the 3DS.
Every game on this list is available on the eshop. Several are eshop exclusive. If you are to pick only one game out of all of the ones I mentioned, get Pocket Card Jockey (eshop exclusive). Again, it's a gamefreak game so if you're a stickler it may still count as a "nintendo made game"... in which case go get Theatrythm.
