Working in the field, I can offer some advice:
Due to the technique only being based in one way of perceiving depth, annoyances cannot be gotten rid of. They are inherent to the technique. Your eyes must be focussed at screen-distance, which will always upset your brain a bit, so filmmakers try to keep the important bits at similar depth when cutting from one shot to the next.
Supposed to make it easier on your eyes, but upsetting to your sense of scale and depth relations.
Keeping realistic depth would require readjustmemt, brain wise, feel more realistic, but also less... Fluent and immersive.
Also, filmmakers adjust depth to their liking and for dramatic effect, which again, screws a bit with your perception.
Then there's the problem that there can't be anything at infinte distance, i.e. due to the fact that you're looking at the screen cross-eyed, the depth on distamt object has to be reduced, giving the strange impression of looking at a wall, on which the horizon is painted on. Having a lot of depth in the foreground ammeliorates this somewhat.
Reflections in transparent things, like a glass window, will not work properly, by definiton, and give conflicting depth information, as you can't adapt focus yourself, watching the film. Transparencies in general are a problem. Lens flares tend to poke your eyes out.
And finally: where you sit in the cinema decides how intense the depth effect will be.
The further back, the more gigantic it'll all appear. So if the 3D is too much, move to the front.
Personally, I've always been very sensitive to depth information, i.e. my brain would easily generate a precise 3D image of something just from parallax motion. I'd be able to see if details on a spaceship had been modeled or just painted on. That made VFX a bit hard for me to watch, as I'd notice the shortcuts.
In modern cinema, buildings and such are often just 3D-cubes with the photo of a house slapped on, and then added into a part-greenscreen shot.
In 3D, they do a similar thing, mainly to be able to adjust depth to the director's liking, but That only makes it even easier for my brain to see that things are often not properly modelled, but -say, the moutains in EVEREST- they get the overall shape right, and just don't care about the small surface features. The mountain looks pretty smooth to me. It's just lacking the detail, while trying to hit me over the head with the large scale.
I find 3D interesting, but highly distracting.
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I can read facial expressions. I did the test.