What you're referring to is professionally called "tactical reload", and for an in-game implementation, you might consider actually "changing magazines", i.e. let's say, for instance, you start with 5 magazines of 30 rounds each.

You engage the first battle and fire 20 bullets out of that magazine. When you reload, the game will retain that half-emptied- 10-round-magazine for you, and switch to the largest magazine at your disposal. So on until you finish your bullets.

When you take an ammo pickup or reload at a weapon locker, regardless of whether you still have ammunition or not, let's compare that to when an actual soldier re-equips himself during a regroup - simply refill all magazines he has, perhaps get more if he can hold them. This goes in line with how ammo pickups and weapon lockers already work.

I see that as far more realistic, challenging, and interesting, than the "arcade" implementation BWpro currently has to offer.

One drawback I can see: In the heat of the battle you find yourself having 5 mags with 1-5 rounds each, which is definitely a possibility considering the implementation I suggested above. A solution might be to allow players to "collect" all of their remaining bullets into 1 magazine, of course at a certain time penalty like while reloading, only factored by the number of bullets in question as well.