From an inventory management standpoint, they could just implement FFXI-style "quivers", which were a low-stack item that, when used, created a full stack of arrows. For example:

I have 23 "cobalt arrow quivers" and 0 cobalt arrows.
I use 2 cobalt arrow quivers from the Use Item menu.
I now have 21 cobalt arrow quivers and two stacks of 999 cobalt arrows.

This immediately solved pretty much all of the ammo inventory issues in FFXI.