I'm not certain there really is a 3D Zelda vs 2D Zelda thing anymore. I suspect given that Zelda is an adventure series driven by puzzle/exploration/narrative, it doesn't make a huge difference for the fans whether the gameplay is full 3D or top down 2D.
I mean if we look at the last ten years of 2D Zelda, what do we have? 200k+ for Minish Cap, 900k+ for Phantom Hourglass, 700k+ for Spirit Tracks, 400k+ for ALBW. It's all over the place.
The last ten years of 3D Zelda? 500k+ for TP, 500k+ for OoT3D, 300k+ for Skyward Sword, 40k+ for WW HD, and now a 200k+ opening for MM3D.
I'm not sure we can really project much about 3D or 2D Zelda from these numbers. In the last ten years, we've definitely seen 2D Zeldas sell better overall in Japan, but I think considering the 200k+ opening ALBW had, the legs were pretty disappointing. We'll see if MM3D fairs any better on that regard. In the end though, I don't think it would translate much to success on WiiU, given the disparity in userbase. No one was interested in the WW HD release, but yet people are all over OoT and MM on 3DS.