Some of the weapons can only be had via the factions.. Some of those weapons happen to be at the top of their class for legendary weapons. Plus after the DLC there will be even more. Why is it that 4 factions only take crucible marks and one faction accepts Vanguard marks? But yet you can gain rep for 3 of the factions by doing PvE stuff. I think at a minimum the 3 factions need to accept both. If you can gain rep from both PvE and PvP they should accept both currencies.