Even with the New 3DS, which had MUCH BETTER tracking, the 3D for me would eventually get annoying and I would turn it off. I think with 3D TVs and Nintendo continuing to put less of a focus on the 3D as the 3DS' life progressed (compare Super Mario 3D Land and A Link Between Worlds back in 2013, to two of the most recent releases (Warioware Gold and Kirby's Extra Epic Yarn) having none at all*). They were probably also tired of parents thinking the 3D will blind their child (hence the need for the 2DS).
All in all, it was a neat gimmick, and that's totally fine if you like that gimmick (I say that with no condescension), and maybe there will always be a small audience that really liked what 3D offered, but it's clearly a niche market and most people that wanted an immersive visual experience have moved onto things like VR, I presume.
*Luigi's Mansion 3DS had 3D, and that's a game where it totally fits because the room structure of that game is already so similar to little dioramas.