Make the default factions more powerful and have epic space battles. Both factions' resources should be roughly calculated. For example, when the trading guild looses a big battle, it wont be able to muster that many ships for the next battle. There should also be systems controlled by the factions so one can take over the other's territory.
The player should be able to do missions for rewards to help either faction. And there should be rewards for it like faction points. Once the player does something for either faction, their loyalty for one faction goes up and the other one goes down. Once you reach something like 100 loyalty for a faction, you become allies, and the other one declares war on you. You get benefits for the faction you are allied with, and both should be different. The state of the war would change depending on the player. If the player destroys one of the factions, the faction becomes a rebel and the dominant faction becomes like the empire in Star Wars. The player can then choose to either help the Rebels or crush them down. The rebels will have more resource gain and use guerrilla warfare until the tide has changed. Then they will become what they were. If the player desires to suppress the rebels, he/she can do so, but over time it would become harder to a limit.
Once one of the starter factions are dominating so much, they would be exhausting their controlled territory's resources and would at times steal the player faction's resources. This would guide the player to rebel against the bigger faction. It would basically be a never ending cycle of war and epic battles. Kinda like how the force in Star Wars tries to balance out.
The player should be able to do missions for rewards to help either faction. And there should be rewards for it like faction points. Once the player does something for either faction, their loyalty for one faction goes up and the other one goes down. Once you reach something like 100 loyalty for a faction, you become allies, and the other one declares war on you. You get benefits for the faction you are allied with, and both should be different. The state of the war would change depending on the player. If the player destroys one of the factions, the faction becomes a rebel and the dominant faction becomes like the empire in Star Wars. The player can then choose to either help the Rebels or crush them down. The rebels will have more resource gain and use guerrilla warfare until the tide has changed. Then they will become what they were. If the player desires to suppress the rebels, he/she can do so, but over time it would become harder to a limit.
Once one of the starter factions are dominating so much, they would be exhausting their controlled territory's resources and would at times steal the player faction's resources. This would guide the player to rebel against the bigger faction. It would basically be a never ending cycle of war and epic battles. Kinda like how the force in Star Wars tries to balance out.