An important difference between the two versions is that the IMAX 3D one is 16:9, while the multiplex version is cropped to 2.35:1. So you get to see more in the IMAX version.
As for screen sizes, I haven't seen IMAX 3D but I find the 3D effect is much better when sitting near the back of the cinema. It's harder to focus when sitting in the front few rows.