At present, ships are capable of engaging multiple targets simultaneously, and appear to prioritize the closest ones.
I'd like to propose a new 5x6* compartment called the Combat Information Center (CIC) that would allow more advanced strategies for larger ships, such as prioritizing certain targets, enable salvo fire of missiles or even fleet control (e.g. telling certain friendly ships to engage specific targets, coordinate formations). This part is intended to operate separately from larger control rooms/bridges, but as always, a ship with a functional CIC but no working control room is still uncontrollable.
Another possibility is that control rooms alone (irrespective of size) would only be able to manage a certain number of weapons and defense systems, such that a CIC would be required to raise or remove this limit.
*Dimensions specifically chosen such that they can only be used on medium to large vessels, and the different-numbered sides allows for odd or even number-wide ships