I think my biggest problem is turrets are one-size-fits-all in nature within the rules. In CT up to three weapons can go in one turret but the size doesn't change, for example. I also have a problem with turrets needing to be manned normally.
On the first, it seems to me that missile, projectile, and sand weapons--that is weapons that use discrete ammunition and have to be reloaded--would require more room than energy weapons that don't need space to be reloaded. A turret with more weapons should also grow in size with the number of weapons fitted.
As for manned turrets, I find this to be almost absurd. Sure, if you have a small ship with a few turrets and no centralized fire control (meaning this sort of turret should be heavily penalized for accuracy beyond short range) you probably need somebody in the turret aiming and firing the weapons. On the other hand, any self-respecting naval vessel will have centralized fire controls, and the turrets probably don't need to be manned at all. Reloading, say missiles, is done automatically. Lasers and such don't need reloading. There's no need for a turret operator but rather there's somebody at a console essentially playing a video game of sorts operating one or many turrets. There are sophisticated sensors and a serious fire control computer tracking the target and aiming the guns. The operator is there to determine if shooting is necessary.
I also find the missiles to be badly undersized for the role they're supposed to play. I also think with discrete ammunition, particularly expensive stuff like missiles, you need to have a magazine to store them, and the size should be variable depending on how many you want to carry.