Let's face it, no one really uses the 3D feature unless they just want to see one scene. After that, they never touch the 3D again.
...Allow me to be the odd-person-out in this thread, haha.
I almost never turn it off when I play Animal Crossing or LoZ - OoT or A Link Between Worlds.
With OoT I only ever did if I was excessively aiming by moving my 3DS around instead of using the stick, because if it's not perfectly lined up with your eyes, yeah, it starts to hurt after awhile. But that really only happened in the water temple because of the hookshot, and I still kept it on for most of the temple. If it was just to pop off an arrow or two for a puzzle, then it stayed on while I moved my 3DS - wasn't much of an issue. I actually preferred how everything looked in 3D, not just the scenes where Link picks stuff up and it rotates above his head.
(Speaking of - Nintendo, why did we get gyp'd on our gym badges in Pokemon? They rotate in lame 2D.)
As for ALBW, I don't really remember turning it off at all - but I'm sure I did for something. At least just for the stupid baseball mini-game.
With AC, I adore how the animals look in 3D. The whole world looks so neat. Especially when they celebrate completing a PWP - the confetti looks absolutely fab in 3D. Though I do turn it off when I go to the island to catch bugs - that's
work, not play. But that's about it.
On the flip-side, I almost never even bothered to have it on for Pokemon 'cause you can barely make out a difference (well, I really couldn't). Perhaps for a few scenes. Maybe.
BUT, I don't really have the issues that you (or others) have pointed out. :c
I don't get a headache from it, nor does it strain my eyes at all. I haven't found myself needing to awkwardly stretch my console farther from my face that I normally/comfortably would. And, as others have stated, I'm usually lounging back in my bed or on my couch when I play, but I've only found that to make it easier to prop it up and line it up perfectly while staying comfy-cozy.
It looks neat and it's comfortable for me to look at it for hours on end, so I use it regularly.
/shrug