I didn't have a 3ds when it was current because of getting a headache the one time I tried one, but I bought a new 3ds last year and I have no issues with having the 3d on for shorter gaming sessions. The eye tracking seems to be a huge improvement for me.

I've played Virtual Boy games on my 3ds and it's pretty amazing. You're right that due to the 3d being optional in most games means they couldn't really use it in gameplay, but with the Virtual Boy games, those were designed for and must be played in 3d. It really made me wonder what could have been for the 3ds if all the things about the hardware that made the 3ds special were used in more creative ways.