I still play my 3ds almost exclusively with 3D on. My uncorrected vision is bad enough that I have to turn it off if I'm not wearing my glasses.
However the AR of pokémon go actually makes the game harder IMO, so it's only on in the rare instances I feel the need to take an in-game photo.
Also, pokego is a significant battery drain on my primary device. I feel like leaving the camera on all the time would just kill the battery faster. OTOH I don't really care if the 3d effect kills my 3ds faster. My gaming sessions aren't as mission critical as my phone battery.