I agree that graph layout tools could be much better. My main comment was to address what I felt was a blanket dismissal of the paradigm in the primary post.
I think the way graph layout should work in visual tools is that it should be domain-specific automated layout with user adjustment. However, the tools aren't anywhere close to that. And in fact, I have struggled to find existing graph algorithms for this stuff. None of the graph layout algorithms I have found can take user defined constraints as input, and they definitely cannot take local, manually adjustments. There's a lot of work to be done here, but it doesn't seem like anyone is interested.
I think the way graph layout should work in visual tools is that it should be domain-specific automated layout with user adjustment. However, the tools aren't anywhere close to that. And in fact, I have struggled to find existing graph algorithms for this stuff. None of the graph layout algorithms I have found can take user defined constraints as input, and they definitely cannot take local, manually adjustments. There's a lot of work to be done here, but it doesn't seem like anyone is interested.