Well here's a possibility for a third faction that's not really a full faction.
Campaign mode. Just like in Empire at War there sounds like there will be neutral systems that have to be conquered. Why not include objectives that involve clearing out pirates? Maybe they have a space station or a few that are decently armed along with several squadrons of fighters and maybe a corvette. In these missions either a DM (if that group is running a DM) or someone from the other team controls the pirates.
So maybe in a future campaign, if they ever do one, they could do the outer rim conflict. Instead of new titles we get maybe two corvette models and six squadrons along with everything else you get in a campaign. So pirate bases are included stuff like that. Set the cost at $50 to accommodate the models.