3D presented in 2D is bad

Theoretically speaking, if you present 3D structure in 2D,
you will fall in one of following situations:
1. something hide behind some other things.
2. in order to see it, you need to shift it. the orentation has been changed.
3. you lost information in one dimention, user will not be able to figure out informatin for that dimention by looking at your graph.

You can only present graph for modified arrangement.
Because you already delete, cut, modified information to make sure we don't have 3D information (it only have two sheets, not three, not one, just two)
And user understand the information in the graph only contents two sheets, they don't need to translate back to 3D in mind.