Walter Murch explains to Roger Ebert why 3D movies will never succeed due to the physical realities not matching what our eyes and brains expect. It's quite simple when you think about it. In a 3D movie, our eyes aren't focusing on the point they are converging on.
The secondary effects he mentions I've already noted myself, e.g., the 3D view makes the screen effectively smaller. I've already concluded it's a waste to watch a 3D move on IMAX for that reason. Scott Wilkinson aruges effectively that 3D IMAX is worth it because the resolution is higher, they use two projectors making the resulting movie brighter, and the screen is more likely to fill more of your field of view.