I also had issues with node density. The way I solved them was by adjusting the forces between the nodes, particularly the repulsion and collision forces so that there is is no superposition. Values too high or too low can make the simulation chaotic or too dense, while others make it more fluid or faster to stabilize from an initial seed.
That being said, if it was a bigger simulation I probably would have had issues keeping the performance, and it's possible I would have considered a different engine.