I was hoping you'd request a nice tiling-preview mode or the like
That said, a node based hierarchy sounds very useful. But fear you're looking at completely other software. Or after effects. Or Combustion. They do that non-destructive non-linear thing wonderfully.
Best not to encourage them to make 10 different versions of Photoshop. It will lead to more grief for the customer than anything else.
Smart Objects I believe are going to be extended in the future. It may be possible for example with external linking and auto-updates, to engineer Photoshop in a more powerful way to do what you want in the future.
Whenever I've worked in gaming environments I've seen people doing complex and file heavy tasks, without even knowing how automation and Actions work. An appreciation of how much a knowledge of these things could streamline workflow is essential. A great deal of what you need may already be there, without you realising it. Element and file hierarchies agreed no, thats not there.
You want Substance from Allegorithmic. What you describe is not really something PS was designed to do.