The shader system should be converted to the same system that armor and weapon mods currently run on. When you get a shader for first time, it's permanently unlocked and in your inventory, When you want to apply it, you just pay a small amount of glimmer.
I don't think anyone enjoys the laborious task of deleting huge stacks of shaders. This has been a problem since early D2, and I think the new mod system is a good template to fix it.
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This is a good suggestion, but the problem with it is it gets rid of the artificial grind bungie has planned with shaders. Spend glimmer and legendary shards for shaders, then you grind to replace those shards and glimmer buy grinding, then rinse and repeat. So i never see Bungie changing the shader system.