I think Arena or match-making of some sort could only work if it was not all the time.
Think, say, daily a NPC with a special once-in-a-day mission appears and some players (say, 4) are chosen somehow to go into the mission somewhere (because you have to be stealthy or everyone will know and swarms aren't know for being stealthy). There in the mission you meet foes from other faction in same number.
One place with equal ammount PvP that worked great was Sierra Caves in FOnline2, my favorite FOnline dungeon so far. Maybe having a limited version of it can be a nice PvP and PvE experience.
Swarm vs Stalker is the default pvp scenario in AOP.
That could be a fun arena scenario:
20 dudes (Swarm) vs one dude (Stalker)
Swarm uses crap tier 1 equipment, but they have total numbers superiority. They have to co-operate to defeat super-stealthy and advanced foe.
Stalker is alone, but he has top tech and a magical stealthboy that allows him to pull Predator-style shit unseen since the early days of AoP. Stalker has to be stealthy as fuck and ambush the Swarm, one by one, before it finds and kills him.