TL:DR: A system should be added that allows pilots to customize their aircraft's weapons load in the presence of an ammunition truck, similarly to this mod in ARMA 2 (but having each weapon be individually customizable within weight limits and with a real GUI) http://www.youtube.com/watch?feature=player_embedded&v=0baCog8jjvI#at=89
One of the goals of ARMA 3 is greater customizability, hence the changeable clothes, weapon attachments, etc. In real life, each type of helicopter/aircraft doesn't have a fixed loadout of ordinance. AGM missiles can be swapped out for A2A or laser guided bombs or even loads of dumbfire rockets, as long as the loadout doesn't exceed space and weight limits.
I am suggesting a simplified version of this for ARMA 3 - customizable aircraft loadouts. Aircraft weapons pylons could be slots similar to the attatchment points on guns, meaning with a specialized ground vehicle one could swap out weapons on a grounded helicopter/aircraft. It need not be too complicated, as each aircraft could have a weapon weight limit and each type of weapon could subtract XXX pounds from the limit, making it impossible to make overpowered loadouts.
In summary, such an addition doesn't seem to be too difficult to make, since most of the work is already done with the weapon attachments, and it would greatly increase customization for aircraft, immersion, and pilot enjoyment.