Is there still a reason to keep them? If there aren't going to be upgrades within a weapon or armor piece that boosts the defense or attack power, what is the point of having them? Is there any possibility of them being worth anything like they did before someone could purchase them using Crucible marks or Vanguard marks?
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Perks....that's why you upgrade them
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If you haven't fully upgraded a weapon or piece of armour, then you should keep them just to upgrade them. THEN ascend them.