I...don't quite understand what you're asking because the games themselves seem to answer your questions.
There are already cruisers, corvettes, frigates, destroyers, juggernauts and the Colossus in FreeSpace. Not to mention gas miners, AWACS, transports, freighters, medical ships...what else do you need?
Fighters can still dominate warships in FreeSpace 2. A wing of assault fighters can take out a cruiser with thousands of people aboard. A few wings of bombers can take out a destroyer with ten thousand people aboard.
Do take note that since FS is a space fighter game where the player is a fighter pilot, the balance in the gameplay is skewed in the favor of the player (fighter). I highly doubt it a single bomber wing can take out a destroyer in the background fluff.
That said, fighters are excellent for patrols and pirate hunting duty. A wing of fighters can cover a larger area than a single cruiser - it cannot be in 4 places at once and is significantly slower.
