Rather than PvP FATEs in PvE zones I'd rather see the creation of a set of PvP focussed zones. PvP focussed zones would be very similar to PvE focussed zones, but with a story line component focussed on conflict between the factions. PvP is always toggled on when being present in these zones.

Rewards from quests should give PvP oriented gear, level appropriate for the intended level of the quest. Mining nodes, botany nodes and fishing spots should give resources which are used in crafting of items related to PvP; such as PvP gear, PvP food buffs, etc.

FATEs within these zones could spawn as well, however should be worked out as sequenced FATEs. Where there may either be a direct source of conflict. Or PvP conflict may even be completely preventable. Fortification FATEs could help prevent the countering team from engaging full on combat. Depending on which side would win a FATE first, the following FATE could be decided.