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3DS. I think they did a really great job with the graphics. They managed to keep the original vision in tact while updating it. I actually didn't it changed so much until I looked at videos of the original. Basically, they made the 3DS version look as good as I remembered the N64 version looking, if that makes sense. The 3D is a nice bonus.

Controls are kind of a mixed bag. I like the N64 joystick over the circle pad, and the position of the Z button is more comfortable than L. On the other hand, touch access to items is convenient and things like the iron boots work much better. I also like the tilt aiming, although I like the 3D feature more, so I didn't use it too much.

Being able to play on a big screen would be nice, but portability balanced that out. It's be nice if the 3DS could output to a TV or something.

So overall, I like the 3DS version better.