let me layout for you some of the greatest advancements, that make Wing Commander ships far superior to their FS counterparts.
The warships in the Terran Confederation Navy carry two types of weapon systems: guns and warheads. All capital ships carry guns, but not all of them carry warheads.
As you may remember, almost every ship in FS carries beam weapons, but has almost no defense armament against incomming warheads. (ok, the do have flak batteries, but they are mostly ineffective)
In Wing Commander universe guns are classified into four categories:
Main Battery – these are the largest guns on a capital ship. These usually include multiple anti-matter guns for cruisers, a single one for destroyers, turreted lasers for fleet carriers, frigates, and corvettes. It should be noted that turreted lasers are main battery for fleet carriers, since they do not carry any larger energy weapons. The Vesuvius-class is however, an exception.
Secondary Battery – These are the second to largest batteries carried on fighting ships, for cruisers and destroyers these are turreted lasers. These are general purpose weapons that can fight both fighters and capital ships.
Tierary Weapons – Cruisers (light, fleet, and medium) carry a third level of energy weapons. Basically capship mounted versions of fighter based laser cannons, these automated weapons are programmed to engage any fighter or warship within 5000 kilometers. Tierary guns are considered point defense weaponry because they are normally too light to prove to be any offensive threat.
Close-In Weapons – Gatling mass drivers are considered a capship’s last ditch defense. If all else fails, they have to run the gauntlet.
I hope I could help you...