I really like the idea of animating graphviz graphs. It definitely helps to make them clearer.

I know it's a proof of concept but one suggestion would be to animate the line drawing itself. That's difficult if you're outputting a raster format but if you're feeling adventurous then you could output to SVG and draw the lines using the stroke-dashoffset trick:

https://css-tricks.com/svg-line-animation-works/