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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I don't think using the same system as mods (when applying the shader) would be ideal, since we would have to shift through dozens to hundreds of shaders to find the one we wanted to use. Instead, how about a system where we could pick 10 - 20 as favorites and have those favorites show up in the Appearance screen, and pay for them there. I do agree with it being changed to an unlock system, deleting shaders from the inventory might be quick, but when they stack up it gets time consuming to dismantle them.