I just can't seem to decide. I really want to play the game with 3D on seeing as how I own a 3DS and all I would want to use that capability. However my eyes started hurting a bit after a few hours of play, and I turned off the 3D. With the screen at it's full resolution, I gotta say the game looks fantastic in 2D. With 3D the screen is split resolution-wise and while the game still looks great, there are noticeably quite a few more jaggies or aliasing, which is something us PC gamers strive to avoid. Thankfully in 2D, the jaggies disappear and the retextured (I'm noticing they retextured a ton of stuff) surfaces looks crisp and clean.
Now I am horribly torn on which way I want to play through the game and was curious to see what you guys were falling on.
Edit: So far after some more fiddling around, I am starting to move towards 2D. I've noticed the framerate is a little more stable, but that is seriously me being super nitpicky. Overall the more I switch back and forth, the more I notice the 3D isn't super substantial, although there are some cool effects here and there, like all the fairy shit or whatever floating around Kokiri Village.