Apologise in advance for being a bit long but while its a great game feel it needs an underlying theme to stop being samey.
If any mods out there do already please suggest but I have the following ideas & want to know if possible as new to modding.
Please say if possible or indeed you think sensible.

With bases thinking of starting name with Faction first (3 letters) & M if main base possibly S for secondary base. This would make several things easier.
Base list will group all that factions bases together
Selling stuff easy to see if friendly
Main bases have the best equipment available & need to check the bar occupants for rumours
Secondary bases again check the bar occupants as important info available.
Example if you take gate XXX you had better be working for the Military its a war zone
Also possibly a bit more space round bases to often you get asked to drop your cargo as enter a trade lane.

Is it possible?

Using scan for cargo
Have a trade good (piece of equipment better as no space) that causes a faction to act differently.
Example Bounty Hunter causes Pilots to become legal goods by Police ignoring.
Trade cards (fitted to freighters) causes Criminals whose reason for being is to attack cargo haulers to attack you if in a Freighter Trans so long as have cargo onboard regardless of Rep.
Police card etc.
These could be fitted to ships none transferable or be purchased only at a certain rep level with that faction. Another possibility is its cargo aboard a mission target

Missions
To add variety thinking are these possible.
Destroy base > can do so long as undock able so thinking place more storage depots & certain criminal types will give these as missions.
Game will automatically spawn defenders.
Escort > Really not sure if this possible but your goal is to protect a ship(s) from A to B Attackers would need Cruise Disruptors obviously but if pick routes sensibly normal spawning could produce attacks. Possibly buying a trade good for 1C that you deliver at the other end completes but how do you check the ship survived?
Depending on who you are working for could be protecting a Convoy (Company) Prison Transfer (Police) or even something smaller with important cargo.
Recon > Thinking long range or hostile territory set waypoints possibly with a wreck type object at (dont do anything but give cargo) pick it up & return with the data. These obviously in hostile territory possibly quite long
If given by person can set up so go deep into enemy space then next mission will send on long range destroy based supposedly on info gathered.
Also you can change reps with bribes obviosly but is it possible to set missions to do so. As in gives the normal mission change but applies a second shift.
Have some other ideas.

Faction setup
Using Navy as an example
Navy to improve relations with fastest way will be to kill Enemy Navy Missions otherwise very hard all arms tied to each other rep wise
Faction set up Navy 1, Navy 2, Elite
Navy 1 >Controls bases if possible has no ships can you do that? If not give but only deep in war zone so you do not run into as start say rep -9 certainly as enemy so undock able but that means they will fire on you hence reason need rumour mentioned earlier because these guys hurt.
Navy 2 >Start below give mission status with some missions placed on main Police bases (use person). So when rep improves can start to increase with Navy 1
Elite Navy > Similar setup to Navy 1 rep improves even slower first missions from people on Navy Bases, these will obviously be the ball buster missions.
It will be a lot easier to lose rep with Navy than gain it.

Other factions can be set up similarly with Fac 1 Fac 2. Faction 2 is harder to please & easier to piss off than faction 1 & is placed in Main Bases so has access to best missions & equipment. It also possibly sets up more negatively at start.

The Idea
Hopeful a setup like this allows more of a progression route /story line stuff added only if does something & indeed perhaps remove some to give themes.
Thinking remove one Navy & do a mirror of enemy Navy Companies Criminals, 2 starting points Legal or illegal side it will be very hard to switch few bribes & if possible they will make all factions on the other side Enemies so need to think about it. Trying to set up a sort of career path so easiest to work for certain factions Navy being the Ultimate goal which possibly will also free up some top criminal factions as they are working for

Starting Rep setup roughly for your side
Bounty Freelancer good
Police most Comp average
Navy as above
Criminals Borderline or enemy based on type

Setting up Rep general overview
Bounty Hunters > Tied to Criminals
Freelancer > This is actually to complement Bounty Hunters more a traders Guild tied to companies perhaps with subgroups (tied factions) for different areas of space. With a bit of thought it may be possible to have best trade goods only available if good rep with these guys, if you could set up so get better prices or can only buy limited amounts of trade goods it would be better.
Police >tied to Companies & Criminals add Border Police
Navy > Enemy Navy & very minor links to Police & “Elite Navy” Comp that supply & Elite Navy may have links to some criminals through its intelligence arm.
Criminals > Tied to there reason for being which also determines base placement obviously. Some can be working for other factions & give missions rumours accordingly. Tied to enemy Navy basically trying to destabilise society gather info etc or friends with one mining company attack the others plus of course the general hooligans but try to make there targets more specific. i.e Smugglers, Pirates so mission is cargo A>B or attack convoy supply depot etc.

This means Police protect Companies Navy have little interest in as fighting a war & you have to work to even get access to there bases
Equipment wise
Worst Companies & some Criminals,
Average Bounty Hunters Police most Criminals & the odd Company perhaps with own Police (escort force) as operate in hostile space.
Best Navys but as said some Criminal factions may get superior stuff to & who knows maybe the bounty Hunters have a Mercenary Wing or one of the companies that supplies the Military has some prototypes that need testing.

Systems will therefore be safe as in trade lanes getting more dangerous border edge contested as in war zone plus the Nomads need fleshing out

Sorry so long here but am I on the right track as feel many mods just add stuff without a reason, trying to make it a more tangible universe so the feel comes through a bit. A Liberty Cargo Co will not like a Bret Cargo Co for instance improving one will detract from the other & making cargos more rep sensitive means its important.