I assume you're referring to the Famicom 3d system, which used Active Shutter glasses. Those work by alternated which lens is open and flickering between the two images on the screen. It wouldn't require the red/blue (anaglyphic 3d), which accomplishes the same thing by color filtration method. Active shutter would look better because the colors would not have to be altered. The method used in movie theatres these days is with polarized lenses, projecting overlapping images with vertical and horizontal polarities. The drawback to this method, is that the lenses also filter out a percentage of the light, resulting in a noticeably darker image.