This is opinionated but backed by reason. This is not at all like the debate on health care reform. It’s better to shoot parallel because you will not incur asymmetrical trapezoid distortion which shows up most often in wide angle in close shots. The zero parallax plane can then be set in post by horizontally shifting the left and right images. The downside of that approach is that you will have to crop image area to maintain the aspect ratio.
When shooting your IMAX films parallel was just fine without having to laterally shift because IMAX uses a different compositional theory — different from that used for the usual theatrical cinema. IMAX strives for a so-called immersive effect and the background points are set to be at a fixed 2.5 inches — at least for many IMAX films. Shooting with toe-in will create the geometrical distortion I alluded to but it can be fixed in post with a Pablo — for example. Most stereo rigs do not allow for shooting parallel to control the desired zero parallax setting. They depend on toe-in. Parallel going lens axes can only have a zero parallax control if the sensors or lenses are horizontally shifted at the time of photogrpahy.
The overriding aesthetic concern has to do with what I call stereo timing — the analogue of color timing. There is no way to set the zero parallax plane with complete confidence during cienamtogrpahy because it is impossible to understand how the shots will finally go together at the time of photography. Therefore, no matter what method used, tweaking in post is necessary to get the right stereo timing — or proper image flow and look.