Truthfully, I'm only responding because I find the idea of a game based on distributed revision control systems interesting and amusing.
And a possible disclaimer, I'm definitely not an artist.

First I think, look at the old Windows screen saver "3D Pipes". It's similar to what you are going for in your screenshot, just with multiple colours. I don't know licensing of screenshots of that screensaver, so just look it up in image search if you haven't seen it before.

And speaking of colours, many revision control GUIs have different colours for different branches. I think you should do that - it makes things visually more exciting, and helps distinguish branches.

The outline of your shader was a good choice in my opinion - the smooth shapes of cylinders and spheres can blur together in cases. One thing though is I'm wondering iif the outline of the join from the cylinders to the spheres should be there? It might be a bit too hard to change your shader for that, since you'd still want the outlines for the sides/edges.

Possibly less to do with visiual style, but a revision control system is incomplete without closed branches, and merging branches. Closed branches are usually indicated by a rectangle in GUIs (with normal commits being a circle) which may help things be a bit more visibally interesting as it's another element that exists.
For complex merges you may need the connections to cross over each other. Since your game is 3D, that means that they can go over or under the "main" layer/level everthing else is on. It may look complicated, but some of the repositories I've seen have been rather complicated and messy. Having it so connections for merges can go either above or below the level the nodes are on could actually help things be easier to understand.

I doubt I've been much help, but I hope you manage to succeed in your project.