I think we already have this tool, it's just not a gui but any programming language. I'll quite often create a debug tool to dump out graphviz of something diff

I think we already have this tool, it's just not a gui but any programming language. I'll quite often create a debug tool to dump out graphviz of something difficult to understand e.g. project structures, syntax trees, call-graphs, components of 3d models etc. It only takes minutes. The problem I experience is that the gap between raw data and an elegant diagram is really quite large. You mention layout problems. Hairballs and insane wiring is bad (and sometimes unsolvable without abstracting detail) but something even harder is that layout has strong semantic meanings, not too far from the order of words in a sentence. Even a small neat diagram can be really confusing or even misleading e.g. closely conceptually related things get spatially separated, the most important things get tucked into a corner, utter trivia looks like the main flow etc. Layout is a subtle language all of it's own. In practice I find it requires one-off programs to inject case specific guidance to produce tolerable results e.g. styling certain things, grouping others, complex rules on what to ignore etc. You could wrap up some of these in a gui but it's so computational that it would be a retrograde step.