To gain the title of "Faction Commander" you have to have finished your epic run, put out your LE and do another run similar to the Epic run. I would prefer, if the run involved killing enemy runners, like the old Epic runs, but these runners would have to be epic masters as well, to make it fair, and because "Faction Commander" is a cool title and can't be achieved by killing noobs.

As soon as you achieved the title of "Faction Commander", enemy NPCs will shoot you on sight.
You gain access to Faction specific PvP Missions, like:

CM: All players can access a new menu at the term, enter a runner's name and an amount of Money, the time the mission will be active, and accept to pay the money and add a Bounty mission, that only CM "Faction Commanders" can accept.

TG: Similar to the CM system. Any runner from any faction can add a mission. But you can only choose between enemy factions to TG and enter a number of kills (no names), time and optional a zone.

CA: Again, any runner can add a mission, optional submit a zone, and the amount of CA enemies to be killed. The idea is, for CA commanders to protect this zone from enemies or to go on patrol.

I think everyone got the concept.

It might be needed to put more guards in certain zones, that only attack enemy faction commanders.

Maybe: Show faction commanders' position in the term, if they enter specific zones, that are hostile towards them. (Like show in term when a CA commander is in a zone near to the TG Canyon or in Pepper Park. Show when a BD commander is in one of the Plaza Zones etc)