I think that 3d gaming is amazing! The first time I bought my 3ds and had to give it up, it was weird going from 3d to 2d. Although my pc had far superior graphics, it felt like I downgraded. It was like playing Crysis 3 for a week and then having to go play duck hunt for a week.
It's kind of funny, but I never had a discomfort phase when I first started viewing 3d content. No headaches, no eye fatigue. I've done 8 hour play sessions on my N3ds without a single problem. ^>^
Im very proud of that! It's a graphical enhancement that some people can't or refuse to enjoy, so in that sense it feels like some kind of exclusive club. ^.^
I actually disagree with popout being cooler than windowed though.
Bravely default is a good example of this.
The layered windowed 3d gives it a cool popup book art style that just ins't the same in 2d.