Yeah, stars are pretty far apart compared to planets. You can make 5 or 9 square solar systems instead of the usual fat cross, and it would be an improvement.
Remember that AI only builds cities on plains and grasslands. Also it requires the number of continents to be small, so having mostly water cripples the AI.
You can use forests mountains and hills to make orbits.
Galaxies are relatively flat, so if you make the scale large enough it would make sense that the game is flat. No one would venture beyond the disk.
But none of this addresses the larger questions of what you are going to do for a tech tree. That's much more important than trying to decide how to represent planets and asteroids.