I like the idea. I can see a ruleset entry where only for certain ammo (e.g. shotgun shells), a partially empty clip on hand doesn't replace another partially empty clip in gun, but top it off.
Some details need to be worked out:
1/ Only works if the clip on hand is of the exactly type of the one already in gun. Different shell types (e.g. rubber rounds vs buckshot) would be treated separately. If a gun has more than one type of ammo (e.g. rifle with underbarrel shotgun), the feature will only work if there is already the same ammo (then top it off to clip max) or if empty (then insert it all).
2/ Interface. I think CTRL or some other key while reloading from inventory will replace the existing ammo in gun with the clip selected. Another key combo may need to be selected for a top off versus full replacement.
3/ Proportional TU usage. I'd suggest that the TU used for top off the ammo in the gun be proportional to the number of rounds being added. This is in addition to any TU to move item from pocket into hand (or equivalent), as applicable.
E.g. if clip in hand has 6 shells, and only 4 are in gun (2 free). Then the total TU cost is TU of moving item to hand + 2/6x(TU of normal reloading).
4/ This can be applied to shotgun shells (not drums or magazines), some pistols (loose rounds, not quick loaders), some belt ammo (maybe), some quivers (arrow holders), maybe some drum grenade launchers.