While 3D certainly never took off (though I'm happy to see Nintendo hasn't given up yet with New 3DS and the improved 3D viewing angle) I'm sad to see it slowly fade away again.
While the results vary depending on genre and developer implementation, unlike VR 3D can be applied to traditional games. Though that might be why it never took off (scare stories aside): there was a distinct lack of exclusive 3D content, it was always optional. VR promises entirely new experiences, 3D didn't.