Need to find or buy magazines for particular gun types (pistol/smg and rifle at least) and maybe caliber (but I wouldnt), need to preload these magazines before combat (loading an individual bullet in combat would cost like 10-15 AP), and you can have so many magazines "ready" (loading one from your backpack would cost x2 as much or more). Various items/feats could increase how many magazines you can have ready (pouches, web gear, special belts). Special magazines (like extended, drum, double-mags, etc) would be rare/expensive (and obviously not an enhancement anymore) and could potentially come with drawbacks.
Primarily this would be a nerf to burst builds as it would limit how many bullets they can throw downrange in a single fight. Also ARs need a close-range penalty!
You could do something similar with other weapons, such as "energy cells" (battery magazines basically) for epistols or shock melee weapons. Pre-loaded energy cells = more damage when EMPd.