The AR of Pokémon GO is the same as the 3D of the 3DS - it was a big part of the promotional material and hype for it but a year after release everyone has it turned off.
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.
Just like with AR functionality on phones, the functionality on the 3DS just didn't turn out to be that useful or interesting for video games.
But since I've never played one for more than 30min I guess I can't speak on that.