Sure, Nintendo says good-bye to 3D.
Like they said good-bye to 2D Mario after the SNES. Until they welcomed it back on DS with NSMB, with great success.
Like they said good-bye to sandbox 3D Mario after Sunshine. Until Odyssey, when they'll welcome it back.
Like they said good-bye to cel-shaded Zelda. After Wind Waker, they gave fans the realistic styled Twilight Princess. Then they welcomed it back with Phantom Hourglass on handhelds, then Skyward Sword on consoles. And again with Breath of the Wild.
Nintendo tries something new, it gets mixed responses. So they try the opposite, or go back to something old and safe, like 2D Mario. Until they try again. It's a never ending cycle. Old new is the new new yet again. Their customers are a lot more conservative than Nintendo.
The 3DS was actually Nintendo's 3rd time to try 3D. It was of little importance on Famicom, they got burned badly with the Virtual Boy and 3D didn't prove to be system selling feature with 3DS. It still is appreciated by many.
When VR starts to take off, 3D will make its return on a Nintendo handheld. I can see them going into both directions at once, 3D on a screen for the younger audience, VR for the 13 year old and over.