Mercenaries- Instead of the bounty system attracting pirates to attack, mercenary fleets would replace them. Their vessels could comprise of a mix of TEC, Vasari, and Advent types. The ships would be painted according to the random generated force they belong too. For example the Red Moon Scourges would have a fiery crimson paint job.
Pirates- These bastards would now have randomly respawning starbases from which they build their vessels and send out raiding partys. Their bases would spawn in non-colonizable gravity well preferably as far away from society as possible. They would target trade and refinery vessels and after destroying a certain ammount, self upgrade. These upgrades could upgrades to their starbases defenses, orbital structures, and non-pirate vessels.
Independents- The Independents are made up of single planetary entities, insterstellar corporations, and massive cargo fleets with zero government oversight.
+Planetary Governments would be simple. They're essentially mini factions, that instead of expanding outside their gravity well, just build up everything within. You could either destroy them and gain the planet or make them give tribute to you. Ultimately conquering them gives you freedom to do whatever you want with the planet, while coercing them gives you a large credit boost.
+Corporations operate differently. They would govern unique structures that like artifacts could be found around a planet. For example one world may have a large articial ship construction ring orbiting around it. The structures is own be Insterstellar Shipyards and for a 10,000 credits can be purchased for use. Once these are purchased they cannot be bought by any other empire. They can be destroyed however, and once a certain time has passed, rebuilt by the company in question to be purchased again around said planet.
+The Cargo Fleets would simply be the ability to supplement your own trading force with larger idependent vessels. They could be purchased on the diplomacy screen under a title of SEEKING EMPLOYMENT. You would be given a courtesy screen of the vessel and how much it will increase your trading power. The larger and more effective the ship is, the more expensive it will be to procure. However, once it is aqquired it will immediatly appear plowing the space lanes under your banner. To insure some valid chaos, the vessels should be as every bit vulnerable as your mudane craft. This shouldn't matter as as long you've got the money, another willing space captain will lay down his or her life for your profit.