I proposed something similar to this a few years back. My rationale was using ST:DS9 as a model. Large Starfleet+Klingons Vs. Dominion+Cardassians. Dominion weapons can pierce shields of all enemies, except DS9 itself which can stop their beams. So, all weapons and shields are normal except Dominion weapons which have a piercing flag, but you need a way to block piercing weapons from going through DS9's shields. Rather than simply having a "shields cannot be pierced" flag to DS9, I figured that a numeric piercing value and piercing defense value should be included. I had it where in order for a weapon to pierce a shield, its piercing value must exceed the piercing defense value of the enemy shields. Shields would have a default value of 0 and all weapons with the exception of beams would have a default piercing value of 0, with beams having 1. The concept of partial piercing (as proposed in this thread, from what I gather) didn't cross my mind.
On the subject of shields however, it occurred to me that it could be integrated into the often-proposed-and-discussed-but-never-developed Tertiary Equipment System. Tertiary Systems (for those who don't remember or weren't around then) allows the instillation of additional equipment into a fighter from the loadout screen, or something similar. An example of a Tertiary system is a cloaking device, but could include things such as extra primary or secondary weapon packs, jamming devices, etc. The tertiary system could (if ever implemented) allow default subsystems to be swapped out by the player. For example, (again from DS9) the Defiant's shields can't protect it from Dominion weapons, but a new shield gets designed to protect against it, which is made available to the player to swap out before the mission. The defensive values of each shield subsystems available would be defined in the tertiary tables, including perhaps a higher energy draw on the rector. That said, you could even have a swappable reactor later in a campaign, making more power available for more powerful weapons and subsystems.