Here's my idea on how this could work:
We could use the Steam Workshop to implement our own civilizations. Say for example, there could be an entire page in the game on it. Like Spore, there could be some kind of "Creature Creator", or a simple version of it. It doesn't have to have many features on it, just enough to make it fun.
Then, we could change on what planets they could live on (1 only, 0.9, 0.55, etc.) This could be done using the Likelihood of Life index. City lights could form on the planet they inhabit, and little particles (ships) could detach from the homeworld and settle new planets, creating city lights on them.
Little wars could go on, and the particles would "engage" each other, and destroy others. Space stations could be created, that orbit around planets/moons/etc. Dyson swarms could be created near stars.
Another good thing that could happen is making objects and bodies stay still. I mean, no colliding into each other, just staying completely still so we can make simulations that look nice. Or at least make stars stay completely still so that planets/moons/systems don't fall apart when they get near other stars due to gravity
The idea may sound too overzealous, but I would like to see the Devs try this. Who knows? It would make the game more popular.