Didn't think I had anything to add to this topic, but I guess I do! I made all sorts of compromises when I was using 3D Vision. Some games worked well with the technology, but many others needed tweaking. Shadows would often need to be turned off, for instance, because they would be drawn at screen depth instead of being as far away as the object casting the shadow. Sometimes sky boxes were revealed to be only about 20ft above your head when you got two eyes to triangulate on the clouds/stars. Fancy post-processing things would sometimes go nuts, too.
I would turn them all off to get the 3D working. It was well worth it to add another dimension to the gameplay!