To solve the Quiver system, I'd recommend using some kind of "Satchel" system:
Each character sheet has say 3 satchel slots, which may only contain ammo, throwing weapons and consumables.
When a character uses the last ammo, throwing weapon or consumable from his hand, the items in the leftmost satchel will move into the now empty hand. Say an archer has fire arrows equipped in his offhand and poison arrows in his satchel. The moment he fires the last fire arrow, the poison arrows move from his satchel to his hand. Same thing for consumables and throwing weapons.
The auto-pickup system should pick up all items that the character shot/threw, not just the last type. When picking up an item, place it upon the current stack if the character already has an item of that type, or in a free hand if not. If both hands are full, put it in the leftmost satchel slot. If the satchel is also full, leave it on the ground. Of course, when shooting fire arrows, the character should also automatically pick up regular arrows (which most likely would go into the satchel, unless the character shot every last fire arrow he possessed, and now has a free hand).
This should solve the issue with multiple arrow types and not enchanting them to prevent the auto-pickup system. It also makes it a little easier early on where you have only a few items of one type, allowing you to switch to another type. If I can hold 12 rocks to throw, I should be able to hold 1 rock and 1 shuriken to throw.