maybe its not a planar graph so he wants to create a cube-3d-visualisation of the graph
I prefer a 3d ui because you have one dimension more and better support for visual effects.
the basic visualization of a graph can be 2D but represented through 3D objects.
look at the picture. The p2p network contains the data on the picture.
the x and z axis would be used for graph representation. y axis would be a filter function. If you move on y axis it will show only you tube content or wiki articles or torrent files (for example).
The next possibility is to rotate on the x-y-plane which could be used to switch between view modes (view the graph, configure interconnect, view stored bookmarks, show installed plugins and so on).
The game flipside gave me this idea how to represent data and functions on data in an intuitive way.http://www.playflipside.com/video.php