Why don't we have fully three dimensional integrated circuit layouts?

Im probably the wrong person to give a long winded answer - but it has to do with the way silicon is turned into an ic. Specifically through deposition, and etching. Modern ICs do have many, many 2D layers and get modeled and viewed in 3D - but its all still built on-top of the substrate.

Simply put design is done as multiple 2d layers stacked because thats how the chips get manufactured. For anything more 3d to be useful we would need to be able to manufacture in 3d too (which is hard, and analogous to printing atoms).