Just as some background, I've had scope setups since 2006 and I'm sure I don't need to convince anyone here how great they are for HT, especially when the use is primarily movies. Watching my JVC RS55 from 1sw, I love the immersion and detail of 2D scope films and 16:9/1.85 becomes just the right size as well.
For 3D it is a different story. 16:9 feels like a great size, but scope 3D gradually started feeling more and more uncomfortable to watch. It is also a known fact that as you sit closer to the screen, the apparent depth of the 3D image decreases. So recently I started zooming scope 3D to just a few inches wider than my 16:9 image, maybe a more CIA relationship. It was immediately a big improvement in 3D depth and comfort of viewing (And yes, I was initially hesitant because it just felt wrong not to fill the screen with a scope image).
As it turns out, this change has totally renewed my enthusiasm for 3D. So much so that I just picked up an Epson 5010 for mostly 3D duties in a 2 projector setup. Really a fantastic upgrade over the crosstalk and flicker filled JVC 3D, and I've continued to use the smaller scope size with great success. Even the black bars have not been an issue since through the glasses they are usually very dark. And watching through the glasses kind of makes you focus more on the image and less on the surroundings/black bars.
So for my setup, the advantages of zooming scope 3D smaller are:
More comfortable to watch.
More apparent 3D depth.
The edges of the images are visible on all four sides which is important for 3D effects, especially on popouts and foreground objects. Often in a scope setup(mine included) some overscan is used to fit all ARs to the screen, to hide pincushion, etc.
The image fits inside of the glasses better.
Brightness is increased, which is always a consideration for 3D.
Never seen this topic addressed, so I thought I'd throw it out there...