Like Burnside said, my understanding is that laser and energy weapons are more efficient, but less effective.
Kinetic/projectile weapons are more expensive and cumbersome to operate because you need to worry about ammo more, but much more effective.
Do energy weapons recharge from a ships reactor or do the batteries need to be replaced when spent?
I could see lasers recharging over time, filling a capacitor that effectively works as a slowly refilling mag, and plasma being something you need to replace. Maybe plasma weapons would need a mix of power supply (batteries) and an ionisable gas (fuel tank/mag).
Personally, I don't like the idea of a universal ammo box (like Empyrion, Space Engineers, etc.) and prefer the idea that after combat, fighters and their specific weapons need re-arming. Much more realistic this way.
This also gives carriers and support ships a role in large fights, allowing for re-arming, field repairs, etc.