I propose a "faction" system that guilds must join as whole. This will allow for some interesting battles in open-world zones. Make it a sort of open-world "mini-game," if you will. This will allow smaller guilds to ally with larger ones to destroy large guilds in other factions. I think that with the current game population, 2 factions would be optimal. The PvP T4 trophies would simply be a more rare reward than PvP T3 trophies, and would result in a player having approximately enough trophies to buy PvP T4 gear when they reach the appropriate level, if they regularly complete daily PvP faction quests.
Instead of actual loot drops, the trophies, AA prowess, and a large portion of PvP XP will be rewarded by accomplishing daily PvP faction quests, such as killing a certain number of enemy faction players. These quests should be on a reasonably long CD (perhaps 12 hours) for two reasons. One, it'll allow the more casual players to keep pace with the players who never work or sleep. Two, it'll prevent guilds from farming each other simply to gain trophies and PvP XP. This would be a fantastic system, because it will promote PvP in all open-world zones, anytime, anywhere. It would also be a great replacement for Shrines of Bori.
One more thought... guilds should be able to drop out of or change factions, with a 24 hour CD before joining another faction. This would give guild leaders and their highest-ranking officers more control over the destiny of their guilds. It'll also make for some very interesting "Game of Thrones" sort of fun. This will be a great PvP option for Crom server, as well, and still give each guild the choice of whether or not they want to join in open-world PvP madness.
Best of all, this will allow PvPers and semi-PvPers, who went to Crom for the higher mini-game population, an opportunity for some "consensual" world PvP in almost any open-world zone.