I think the sniper-bay style WITH a damage boost is a good way to go Matt. Something as simple as:
"In addition, Large bays receive a DM+4 when attacking targets of 5,000 tons and greater" This means they won't blow away an adventure ship trying to make a cool dramatic exit, but have a specialization that is really really cool.
Also Matt - this flows well for the other post where we discuss how only certain weapon can crit larger ships on Effect of 6+. It creates a good niche for Large Bays.. not only are they your counter to battle-riders, they can also be specialized in dealing more critical damage than raw hull damage due to their in-built accuracy. After all, they are FIVE times the size & Hardpoints for under 20% more damage.
I'm actually feeling really good about making them our "accurate, capital class sniper critting machines".