Can someone translate whatever industry's jargon this is to geek English, please?
A "fade" is a technique in TV and film for changing from one scene to another. The simplest (and laziest) is a "jump cut", in which the image one your screen abruptly changes. Sometimes a fade is done by juxtaposing objects of similar geometry (i.e., pan the camera to a woman's circular parasol, cut to a shot of the sun in the same position on the screen, then pan down to the scene below.) Another option is to fade to black and then fade in the next scene (Tarantino has been doing that for his chapter breaks, and a lot of TV shows, such as LOST, like to fade from black coming out of commercials.)
A "crossfade" or "wipe", is when the image of the next scene is "wiped" over the previous one, like somebody sliding one painting in front of another. George Lucas used them A LOT when making the Star Wars movies.
The problem that Dr. Manhattan was talking about is, when you do a crossfade, you briefly have two images on the screen at once, which really messes up the stereoscopic 3D effect. For that reason, re-mastering a movie like Star Wars to be a 3D feature would be nearly impossible without major edits. If fact, you'd probably need to go back to the original raw footage and re-cut the entire movie.