Thanks for the compliment! The larger graph is basically built by extracting all relationships of certain types (e.g. parent/child, teacher/student, cause/effect) from Wikidata, along with the earliest known date for the items (e.g. date of birth, time of invention/discovery). The layout started as a 3D force-directed layout, but I turned one axis into the timeline. For the visualization, I used (forked) https://github.com/anvaka/pm (which did get some deserved attention here: https://news.ycombinator.com/item?id=40817852 ) and the related ngraph.offline.layout repo.
Trying to answer your final question: there are a lot of things that I should probably improve here, but I've also wondered if this kind of giant graph visualization just doesn't really work for most people.
Speaking of Burke, I believe his book The Pinball Effect has notations in the margins directing the reader to other pages that mention the same node in the graph (whether that's exactly how he thought of it or not). It seems like an interesting attempt to express this non-linear structure in the form of a book.
Trying to answer your final question: there are a lot of things that I should probably improve here, but I've also wondered if this kind of giant graph visualization just doesn't really work for most people.