Here's a plan for PvP "depth":
Incorporate the marker ideas brought up. Have PvP'ers tallies recorded. Tally up internal (same faction or allies) and external (outside faction or allies) Compute a workable ratio between the two to finalize who the top faction PvP'ers are.
Then, (and this is where is it gets good) have a spot in the mod (bottomless pit anyone?) where some factional advantage can be won, defended or lost through the actions of the PvP champs. But, have this area only accesible if their PvP tallies are in the top X% of their faction (X based on total number of people in that faction with PvP tallies) Also, have the bonus that the faction receives be temporary (like a stat or xp boost that lasts for a week).
Now as far as that "spot" where the combat takes place is concerned, it should be a fairly decent dungeon... maybe some back story is involved (lost Monestary or something) and the dungeon should cater to all types, traps, challenging custom beasties (tailored to fight PvP'ers), variable terrain (twisty tunnels in some areas for melee types, cavernous halls for ranged and spell fighters in other areas) Have the whole deal administered by DMs, of course. And finally, have all the disparate roads lead to some central location that inspires PvP conflict at the center. Or for variations, have 5 or so of these Nexi in the dungeon. This way, on separate occasions, different Nexi can be the goal.
You could reward the participants and winners with ammies labeled Gold Medal, Silver Medal, Bronze Medal, etc. (Of course we'd have to assign properties to the medals so they'll be worth equipping.
Oh well... that's the little bit I had for today, discuss amongst yourselves.