Idk about you but I think the power of certain enhanced perks, and the guarantee of getting the exact roll you want, makes weapon crafting worth it.
My main complaints with the system are how slowly you get neutral element for how much of it you need, and that it's too expensive to really do any experimentation. Were those to be fixed I think it would be a perfect system.
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At least half of the enhanced perks do absolutely nothing when you upgrade to them. The whole system is just a waste of time and resources.