Yeah I agree, the size between the nodes is pretty minimal, and hard to spot.
I’d even like a dimming effect, even when you aren’t hovering over the links. Do distant notes would be slightly dimmer. (But not as dim as they go when you hover over a node.)
Have you seen what @akaalias is doing with the graph? If you’re interested in digging in code, you might be able to adjust this yourself. See this thread: Graph nodes size should also depend on word count in addition to no of links