In order to be able to use the graph view I would be great to be able to save graph layouts when they are modified by the user dragging nodes around. This would help to arrange nodes and clusters in ways that make it easier to remember.
It might even be possible to combine a animated force layout with a deterministic algorithm, these days for instance d3 uses a fixed seed to generate the same graph layout after reload.
Using d3 would also allow for instance to constrain the layout of journal dates in a straight line, so that pages and other nodes would lay themselves out along when they were journaled. Maybe using a weak link charge for page <-> date edges.