To your main point: The 3D still didn't feel completely natural. I did not feel like the camera was forcing me to focus on anything in particular, but I did feel like the whole thing was slightly blurry. Maybe it was my position in the theater (off to the right side of a huge Imax screen, rather than dead center), but it detracted from the experience because I wanted to appreciate the details and they were often fuzzy due to imperfect alignment of the images.
It's a huge comment, so here's the relevant bit:
"What Cameron has been doing with Avatar is to shoot in deep focus (no using the aperture and focus controls to blur out the background, a favorite technique for isolating the subject from the environment) but instead create depth by altering the angle between the two lenses dynamically, creating the illusion of a large space in which attention to depth is focused stereoscopically. Until now most 3d projects have kept the stereoscopic distance fixed, which yields the feeling of watching the story take place on a stage in front of one and occasionally having one of the props or actors protrude outwards toward the audience. By varying the angle between the lenses in the same fashion as our eyes, Cameron presents a far more immersive way of experiencing the third dimension."
Your eyes are only 0.1m apart so anything more than 3-4m away isn't really in 3d anyway. Everything in the distance is handled by your knowledge of it's relative size and position - which works just as well on a 2d screen anyway.
Try it, cover one eye and look at the scene, you will see a difference on your desk, but no difference for the scene outside your window.
That's why most 3d movies have lots of things flying at you and other gimmicks - it's because otherwise there wouldn't be much 3d-ness
I would argue though that just because you don't see in 3D at a long distance, doesn't mean that the little area at 3-4m away isn't important for traditional movies. Most personal interaction is at that distance. In fact, a lot of the dialog scenes in movies are shot as though you're standing right there looking the actors in the face. I think good 3D in that range is also what pulls you into the scene and really makes you feel like you are there. There were a couple of scenes in Avatar where this was really well done, most notably when they were in the thick of the jungle and insects were buzzing around your head. That little detail really made me feel like I was standing there.
I have yet to experience any sort of 3D entertainment that isn't (at least initially) disorienting. The need to wear glasses constantly ruins the experience. But even beyond that, the unnatural way the camera "forces" you to focus on things in the foreground also feels wrong to me and breaks the illusion. If the main character is front and center, but I want to stare at the wall right behind him, it shouldn't be blurry. But it often is blurry because of the camera's depth of field. You sort of feel like an unseen hand is forcing you to look at certain things and not others.