The base idea, the engineers, and in O'Brians case, CPO, they made upgrades or enhancements and fixes (defiant) to systems. So we incorporate it. And expand it.
So, ships have the standard load out of gear. My thought being that phasers are phasers. The difference being how many a ship can carry. We bring up the research aspect that allows the onboard engineers and scientist to learn new things. And then apply this to the phasers. Increase efficiency, decrease the energy required. Increase damage, range etc.
An example, stock phaser, the improvements are range, efficiency, damage, recharge time. Each can be upgraded and each upgrade improves 0.5 %. And we allow 10 upgrades in each areas,
So a phaser could be up yo 5% better in each area.