Very cool, looking forward to seeing it in-game

About the system - you may want to reconsider using a weapon as a system, as you won't be able to get the AI to use it. As the player, you also wouldn't see weapon arcs, ammo counts, etc - it's just not meant for that usage. If you want the weapon to be a unique part of the ship, I'd suggest making it a built-in one (like the Onslaught's TPCs).
For the system itself, I think it's a good idea to look at the role of the ship and give it something that either makes it better at it, or shores up a glaring weakness. Given the BRD "glass cannon" theme, a Fast Missile Racks type system - to use in conjunction with the built-in missile launcher, if you go that route - might work. Or something similar to the Accelerated Ammo Feeder, but for missiles (that'd work better if the missile weapon wasn't bursty, but just had lots of missiles and a decent RoF). A last-ditch defensive measure could work, too.
Just suggestions/thoughts, obviously. I definitely wouldn't put a real weapon in the system slot, though, not if you care about the AI being able to use the ship.