Oh I remember the pain I had with restoring references between saved objects in previous game I made (Pixel Pirates 3D) :D
Just like you said, I'm making it simple and may leave it that way with a bit of storytelling:
'You're not loading the game, but moving through time and space, generating energy blast wherever you happen to appear. Everyone there stops in confusion'
Going back to progress I made - I have already saving of station grid (build modules & trusses), mining settings and units. Before releasing first version I wish to add saving of devices (with their content), planned constructions, earned cash and current cycle.
Second release will have asteroids, contracts & visitors