Make your factions complementary
Factions are omnipresent in games, so make sure your factions have enough contrasting elements, such as technology levels, customs and racial traits to make them unique. For example, if you have an industrial, technocratic empire, it can be interesting to oppose it to a primitive, spiritual tribe. This contrast can create interesting situations when your important characters, who come from these vastly different environments, start interacting.
Good character design is about getting your audience to respond emotionally to your characters