I think PvP could be treated as sport/training, where guardians are given standard issue, crucible specific gear that could be leveled up via crucible, if crucible is what you prefer. There could be some things that cross over, maybe ascendant mats, weapon packages, PvE buffs similar to the Nightfall buff, etc., but ultimately would help balance PvP and avoid any detrimental influence to PvE from said balance. The Crucible bounty board could be a separate board with stats and results showing which factions are excelling, and weekly crucible events could have faction winners in which participating members of said faction get a discount or item package.
So much promise...so much waste.
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Mmhmm, have PvE weapons do actual damage and effects and have a slew of balanced generic pvp weapons to choose from. Keep the balancing unique and separate to pvp or PvE. Reduces the amount of disappointment you experience once you fully level a weapon only to have it nerfed.