3D has a lot of practicality to it. The perception of depth, for instance, can train a person's eye to perceive depth of field much more than a flat screen. For physical training purposes, simulation games could actually help some instances of hand-eye coordination. Now that's the first point.
The second point has to do with immersion. Like one developer said, imagine your character is looking down from atop a cliff. The player will be able to much more accurately perceive how far down that cliff really is. Now, if that isn't enhancing the game, then I don't know what is. Of course, it's not going to improve the story, but it will, most definitely, affect gameplay in a good way.
People saying 3D is a fad is like the old days when people said color movies was a fad, or talkies was a fad, or stereo sound was a fad, or surround sound was a fad. 3D will become standard at some point. Those of you who think otherwise are simply ignorant.