Up until recently, my nodes simulation had all the nodes colliding with each other with the same force, and each reacting the same way, regardless of size. I've tweaked that a bit now, so a node's size matters when it collides, and so the larger nodes can bully their way around (to some extent) while the smaller ones flit about in between.
It's a little hard to make out in this short GIF, but that's what's happening. Feeling pretty good about these changes!
Oh, and the nodes all look like single-celled organisms now.