I've been leaving the 3D on the entire time with only a few exceptions. I do turn it off when the camera angle gets bad or during the occasional boss fight. I've noticed that when a wall or item or character model is right up against the edge of the camera, the 3D looks way too weird for those bits and ruins the rest of the effect (try walking down a hallway, pushing up against one wall, you might see what I'm talking about as the walls passes the edge of the screen). In those cases, I turn it off. And the giant Octorok miniboss fight, I had to turn the 3D off because the camera just wasn't playing nice with me and that made the 3D effect look kind of awful.
Aside from those cases, I play with the 3D turned on and the slider all the way up. I think it looks fantastic and I manage to slide right into the 3D's sweet spot almost immediately.
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