It's interesting that you mention a more 3D view. We were ideating on this, but it's really hard to get right in a way that the user can understand. This is definitely part of our vision for the future though!
EDIT: Deleted the bit about my speculation regarding Light Table since it's false.
I’m imagining a typical graph might end up looking a bit like this: https://upload.wikimedia.org/wikipedia/commons/thumb/8/81/07... in which case I’d want to have whatever cluster/file/method/object I’m focused on front and center with some visual cues like low-contrast and z-axis perspective that preserves edges to show the “far” clusters that interact with the focal point.
edit to add: as per usual, naming the clusters automatically might be hard.
There's definitely demand for this tool but it looks like it's hard to get it off the ground. Wishing you the best of luck!