Interesting idea. Controls a bit clunky, but I’m sure I could get used to it.
Maybe copy 3D design program controls: use mouse click+drag to orbit around a central point, and wheel to zoom. I think the extra rotation option (Q/E) that you have just helps me lose orientation faster.
I think you’re using an orthogonal camera. A perspective camera might help with intuitively figuring out the depth of nodes in the cube. And/or alter the size/opacity of the empty points: closer larger/opaque, further smaller/slightly transparent.
Improve control and visibility, add some juice, and you’ve got a solid game!