Maybe a system where players can apply to be available for 'commanding' NPC location defenses, someone from the cRPG team who knows the playerbase pretty well ( maybe one from EU and one from NA ) can decide who they feel are capable commanders, then appoint them the posistion.
Then the first commander to join an NPC side gains command and players MUST follow his orders or face consequences, like fines or even temp bans from Strategus battles - permanent if the offense is repeated. If he doesn't show up for the battle the next person who had signed up to the battle that is able to command, will get the command job that battle. Maybe his text should also be a different colour so it's easy to spot in team chat and everyone knows to read and follow orders.
Well, that is just a rough idea, there are many things to be thought of that would make this system better, but it's a solution nonetheless, the only problem that jumps out at me is if there is a decent guy who gets the commander job, but continues to give stupid orders and doesn't really know when to stand and defend and when to push and attack the enemy.
I guess players from the battle could give a rating on the commander, which would be recorded, players who keep giving low ratings to anyone just for the case of being a dick will have that ability removed and commanders who continually recieve low ratings and complaints from many different people and groups of people, i.e different friend groups and clans, will have their command ability removed for being incapable of doing the job properly.
But yeah, just an idea.