Using a map metaphor, the graph view is a world map with the details of a city map. It provides an overwhelming amount of detail that makes it difficult to use without a lot of maintenance and specific design decisions that make it useful. But it’s pretty and I love it!
My suggestion is to add a feature that allows you to hide the details of notes based on their connections. Allow you to mimic the difference between a city map, country map, and worldwide map by using the number of links connects to surface notes to higher and higher levels of abstraction.
Doing this would allow users to freely add notes regardless of design decisions and use link strength as a way to navigate their knowledge.
I’m not aware of any workaround.