Something similarly as in Age of empires II, every civ have special bonuses.
You can made something for youre mod so we do not have anymore many factions with same/similarly ships/fighters.
In main building (building give 2000 resurses) put some bonuses for that faction.
Bonuses can be in %. Bonuses: attack, defense, shields, range, economy, LOS, speed, building speed, cost...