I dunno about you, but I think my idea keeps it simpler and within the sandbox feel of the game, where you can create (opr upload) factions into your game to use. I could see giving factions different behaviors as being viable, but I don't think that they should have many similarities as other games. StarMade ain't Sandbox EVE after all.It'd be a matter of having pre-built components put into the system, and make certain parts compatible with others. I'm also not sure how you got the idea that my suggestion is more about pre-determined factions, rather than dynamic factions (procedurally generated and can change significantly) and my system would easily be able to support having server owners create custom NPC factions since both the generating and AI of the factions would simply be based around a large amount of numbers, which could easily be changed via commands or configs, so it supports your idea as well. :p
I also hate the idea of getting missions from high up the chain of command, rather than immediately being basked in greatness by everyone, you could either be the ruler of your own faction, and control the NPCs in your way, or you can help out another. (these are ideas which I'm coming up with now :p) If you see some miners under attack, or some refuges being caught by police, then helping them out will give you recognition, until it gets to a point in which the faction your helping starts to ask for help, using a similar storyline mission system found in EVE, in which you'll perform little tasks every now and then which'll help the faction in it's current goal. At some point, if you gain enough recognition, you could get yourself onto their government, and eventually voted for by the population. This idea could be very nice to implement in both of our suggestions, as it will allow for more immersion, and make the world feel as if it's a proper universe, rather than a game world.
As for what you suggested in the second paragraph, that sounds a lot like what you do in the game "The last federation" (Do things to gain trust and influence), and honestly, I don't see Starmade taking that sort of political route. The game is, first and foremost, about building ships and stations, and fighting among others over things that I assume will be added later in development.
So I stand by what I said before, I don't believe our ideas are as similar as you think they are.