It depends on what kind of Zelda experience you'd like to play.
If you're a beginner and you like retro-style graphics, The Legend of Zelda: A Link Between Worlds is for you. It captures the style of Link to the Past superbly and is quite generally considered an easy, if not slightly short game and has good replayability. That being said though, if you aren't familiar with Zelda titles beforehand, this one should be a good title.
If you're looking for something more 3D and you've played a bit of Zelda before, The Legend of Zelda: Ocarina of Time 3D is for you. This takes a dive into what was the first 3D hyrule of the franchise. It has a good story, puzzles, sidequests... It's all really good. Although expect some dungeons to not go easy on you. *Looking at you, Water Temple* >.>
However, if you've played Zelda before and want to play something more interesting, The Legend of Zelda: Majora's Mask 3D is for you. This game is by far and wide considered a really creepy title in the franchise. It has sad depressing moments, some fears, a giant moon that will crash into the area you play the game in, etc. But at the same time, it ups the challenges imposed in OOT.
This game is more even between sidequests and major gameplay than other Zelda titles, but it also has much more items to use. Namely the masks of which there are 24 of which all have their own unique gimmick to them, and 3 transformation masks which are essential to the gameplay and let you change into a Goron, Zora and a Deku.
I would definitely say that Majora's Mask for all it's creepy tones it sets, is my favourite title and is very replayable. If you are a stickler for timelines in games though, I'd suggest you play Ocarina of Time first.
So there are your options. There's also the side note of getting the Zelda VC for the 3DS games of which there are 5 of them, but those aren't strictly speaking 3DS titles. They are however fun to play and canon to the timeline.