As of today, one solution could be an alliance system working with major powers plus attached minor powers. For example, these could be:
Major power 1: Russia (Alliance: The Baltic Union) --> attached minor powers: Poland, Sweden, Denmark
Major power 2: United Provinces (Alliance: Belle Alliance) --> France, Spain
Major power 3: England (Alliance: The Commonwealth) --> USA, Prussia
In this way, every player could still choose his or her own allegiance but would be part of a "greater goal" within the three alliances. Pirates would remain Pirates but could be attached to alliances, too (or their clans even delegated and paid to attack a specific enemy).