It's not that 3d user interfaces have been fully explored, but that simulated 3d interfaces on 2d desktops have some fundamental limitations. We already have some amount of simulated pseudo-depth: windows can lie on top of other windows, etc.
The problem is that by the time you get around to interacting with something, you're interacting with a 2d euclidean plane which presents a projection of some 3d model. It doesn't make the plane 3d. You can't reach around and touch the "middle" of an 3d object projected onto a 2d plane. That's a problem. These might be somewhat ameliorated by true 3d interfaces (where the display itself is 3d), but that tech has yet to mature.
If you think about it, even the way we work on our typical desk is mostly 2d, from a topological perspective. I have a pile of papers and some random crap lying around my desk. When I go to grab a document to work on, I don't just reach into the middle of a stack and pull out the right one. I don't have that capability. I need to go and start flipping pages, basically morphing my 2d topology to reveal some object hidden in 3d, and only then interact with it.
That's not to say that all 3d effects and stuff are useless. Simulated 3d is a great way of providing visual cues that we have been training ourselves on since we opened our eyes. That can be a very important aspect of intuitive interfaces.. but fundamentally it acts as a visual highlight. The goodness or badness of any particular 3d interface depends entirely on how effectively the _2d_ projection is.
Thirdly, "true" 3d is actually too limiting. We are forced to live in a 3d world, but our computers give us access to many more dimensions, weirder dimensions, than that. We can provide 2d projections of abstract non-fixed-dimensional objects, like n-ary trees (e.g. filesystems). An example of a projection of that abstract object to a 2d interface would be spotlight. It provides a 2d textbox which behaves in strange and weird ways - a 2d textbox that projects 2d manipulations (type some characters), into an arbitrary traversal of the tree. Compare the utility of that to the utility of a "true" 3d rendered filesystem. What value would that add? Sure, it would look neat, but what extra thing would you gain from it?
There's nothing magic about 3d. Computers operate above and beyond limitations of 3 dimensions, and are currently constrained to expose their behaviour through primarily 2d interfaces. Simulating 3d on top of 2d user interfaces, aside from the "visual cue" aspect, is kind of an arbitrary choice.. not necessarily the best one.
-Laxitive