You're ideas are great.....for PvE.
The problem is the same one re-forging had. Destiny is also a competitive shooter...so even slight differences in weapon power can create significant competitive advantages. So people will attempt to craft the most POWERFUL version of the weapons possible.
So, unless you make a crafting system extremely expensive and extremely time-consuming. It will cause serious balance problems in PvP.
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Maybe just a simple light or element infusion system, would work.
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The custom guns could be "banned" from PvP as to keep it more "balanced"(we all know PvP is in no way balanced)
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I don't know if it will ever be truly balanced if you ask me.
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In all fairness, I am writing this from a someone who's spent most of their time in PVE and to give something for PVE players to do and to create weapons we can call our own. I am very well aware that this could very well lead to everyone trying to create the most powerful weapons possible (which would it be a bad thing at this point if everyone felt super-strong and test each other's mettle against one another?) But yes, I have been discussing this here with other folks what tweaking could be done and how to make this a system that would be less prone to abuse. Such as ranking up with Banshee to unlock this ability, buying the frame archetypes individually for a sum of Glimmer (I have way too much Glimmer as it stands now that hardly gets used) and having the cost of crafting weapons include Glimmer, Motes of Light, Weapon Parts, Legendary Marks, and if you want to add an Element to them, you'd need Planetary Materials.