Major challenges to 3D GIS developments and applications
What are the major challenges to 3D GIS developments and applications, especially, in complicate facilities and surface-subsurface 3D systems?
3D spatial data modeling and realization (raster, topo,TIN, geometry) in one 3D solution system, and then smoothless interoperation in others!
Among those, 3D design models (as 3D CAD models) and some 3D geo-models (as 3D G&G models) also must be considered (even, intergrated), even though those 'geometry' may be too details for some 3D GIS systems...
The techniques and theories of 2D spatial data modelling are not able to fully be transferred onto the aspect of 3D data modelling and structuring. Besides, realizations of "true" 3D GIS spatial system needs a lot of efforts from 3D computer graphics, 3D computational geometry, 3D CAD, close-range photogrammetry, and Lidar, which are extensively taking place in energy and mining industries. 
A basic reference is available below