Yet before this patch, you could get any type of Mark you wanted using upgade materials.
Why give people an alternative way of acquiring marks than yank that option away. When did Mark exclusivity become an issue?
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Maybe Bungie see it as more balanced this way? Before, PvP players had to farm materials to upgrade weapons and armour but PvE players never needed to even set foot in the Crucible to get marks/Faction gear. Now, PvP players still need to play PvE to get Ascendant materials (RNG drops are too slow) but are relieved the tedium of material farming. PvE players now need to play Crucible in order to purchase from Factions.