I played through A Link Between Worlds and it really adds so much to the experience. I tried turning the 3D off and it just wasn't anywhere near as good, the depth just really helps. There are a few other games that make such great use of it like 3D Land and Mario Kart... I just don't want to go back to 2D now.
I know 3D got a lot of hate and continues to do so because the technology has been implemented rather poorly and leads to eye strain. However they finally got it working really well with the New 3DS and it can only get better if companies focused on it a bit more. It also really comes down to how well the game makes use of it, for example Tomb Raider Underworld looked so amazing in 3D, it's one of the few games where things actually looked like they were coming out at me. I could easily imagine Uncharted 4 doing the same thing... though obviously we'll never get to experience that.
I'll just be sad to see it gone, a great concept that was killed off because it was done poorly for the most part. I know we have VR now, but I have a headset and I rarely use it because I cannot be bothered to put it all on and set it up each time. I just want to sit down and relax, something where 3D causes no extra effort to experience if the screen has it built in like the 3DS.