I'm aware this suggestion has been made in the past, this is merely my opinion of how it should be done.
Gunsmith doesn't actually make weapons aside from Exotic quests, I think we should be allowed to commission custom guns from him. Imagine an interface similar to a weapon detail page with empty slots where the perks should be, plus some more for the non-perk components.
[b]We'd need to give him the following:[/b]
[b]* Weapon Frame[/b] - This determines the weapon you get, obtained by dismantling another weapon just like it (e.g. dismantle Queen's Choice to get a frame for Queen's Choice).
[b]* 3 Weapon type appropriate scopes[/b] - Only necessary for Scout Rifles, Sniper Rifles, and any other weapon type that allows you to change scopes on the details page. Won't be necessary for anything that has a fixed scope (e.g. Queenbreaker's Bow).This determines the scopes you can swap between. These are obtained by dismantling weapons with the scopes already on them.
[b]* Misc. Components[/b] - These will be given to the gunsmith to determine what perks are on the gun. In addition, you can choose (to some degree) which columns the perks are on. Any weapons with guaranteed perks (like Exotics or Raid weapons) will have the appropriate spots already filled in and greyed out. These will be obtainable by dismantling existing weapons with those perks.
[b]* Elemental Core[/b] - Also obtained by dismantling weapons, they determine what element is on the weapon. They are only compatible with Special or Heavy weapons (primaries too if that becomes a thing again, I've got nothing against it). Also, for weapons with a guaranteed element, this slot will already be filled in and will be greyed out.
[b]* Other Materials[/b] - Spinmetal, Helium Filaments, etc.
[b]* Weapon Parts[/b] - Will cost 500, he is making it from scratch.
[b]* Glimmer[/b] - 5000.
[b]*Motes of Light[/b] - 25.
[b]* Legendary Marks[/b] - 175 (maybe 200 if they raise the cap).
[b]* Exotic Shard[/b] - 5 of them, but only required if it's an Exotic you're after.
[b]* Glass Needles[/b] - 3 of them, but again, only required if it's an Exotic. Necessary because the player is capable of choosing the perks.
By giving all of this to the gunsmith, he will give you a Custom Weapon Order, and you will receive your gun the next Armsday at 300 Light.
I believe that this feature being implemented into the game would be beneficial, as it would give those who aren't as lucky in their rolls a chance to get something great.
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I had a similar idea and it was just that when you dismantled weapons you would do so for the perks not the parts and you could switch them out to corresponding weapons.