From the article: The Wikipedia entry on depth perception (an excellent read) lists ten different cues that your brain uses to figure out exactly how far away something is. Parallax is just one of them. Since the various movie and television display technologies only offer parallax-based depth cues, your brain basically has to ignore several other cues while you're immersed in the world of Avatar. This is why the 3D…
From the Wikipedia article, of the 13 depth cues, only 2 aren't properly present in 3D films - accommodation (having to focus the eyes) and peripheral vision - and the peripheral vision cue is also missing from regular cinema, TV etc. So are there more things going on here? It seems unlikely to me that the focus of the eye lens is having a big impact.
Not on the list (I think) but what about head movement of the viewer? If I move my head slightly to one side the picture stays the same while I expect to look behind an object.