I feel like I came to a decent place in terms of balancing ballistic weapons. Each faction has strengths and weaknesses in their ballistic weapons, so instead of mounting the strongest ballistic weapon, hopefully you pick based on how you plan to use the ship.
ISA ballistics have moderately high DPS, and high capacity (generally 30 seconds sustained fire) but fairly bad reloading ability. The idea was that much of their damage comes from missiles and energy weapons, so ballistics are generally for finishing off weakened enemies, or fighting an outnumbered enemy after the initial missiles have been fired. The large rotary guns now fire a burst of 20 rounds, and have high DPS to make up for their craptacular range. Hopefully it makes them an option at least.
RSF ballistics have lower end DPS, but good sustained damage, meaning they are a good fit for the rapid fire of RSF ships.
XLE ballistics have not changed too much, they are still the high DPS, low capacity weapons.
UIN ballistics have low capacity, but fairly quick reloads, to fit their brawling style that fortress shields provide. I also renamed some of the weapons whose shell weights didn't really make sense (a 60 lb shell is roughly what goes in a 4 inch cannon. A 2000 lb shell is more like what would go in a 16 inch cannon).
If anyone wants to take a look, you can download it here: <Snip, I'll be making a thread for this soon(tm)>