In an ideal world, the system will automatically set the 3D to its maximum setting based on screen size. What this boils down to is setting maximum separation between left and right channels to the average interpupillary distance, usually around 60mm. Most genuine 3D software can do this automatically. This means that decreasing the screen size would be detrimental because it would spread the left/right images much farther apart than your eyes, causing your eyes to diverge to focus on it, resulting in an almost immediate splitting headache.
Take the Trine games, for example. Objects in the far distance are exactly where they need to be, at maximum separation based on screen size. It's like viewing something at infinite distance, like an actual mountain range fifty miles away, or things like the moon or stars. Why would you want to change that to anything other than perfect?
Now, this doesn't refer to games that "fake" the effect using cheap-ass reprojection techniques. Those are ****, and they deserve to be shat upon. I won't even play them, the experience is so far below native 3D that it's far better to just play them 2D. Gaming is not the same as movies... it's either native or nothing.
Welcome to Rivendell, Mister Anderson.