You're talking about a No Man's Sky type depth of game right with unique planetary systems and then you go to the planets and they contain unique objects. It's quite complex so you're going to have to get used to the fact that it won't be too easy to make.
Whatever method you used to generate the planets, I'm saying if you give the object 'Persist' behaviour then it will retain its values when you return to it in a layout. Somewhere along the way I guess you would have to use arrays though.