Now now... Let's not forget one major thing here... Most cruisers that were still in use during the 2nd Great War were designed during or predating Terran Vasudan war. Now can any of you children tell me what major difference modern fighters have to those of TVW era fighters? That's right, shields.
You go against any cruiser, including Aten, with a wing of unshielded fighters, and you will be challenged. Especially in FS1. IMO FS2 did terrible things to blob turrets making them little more than waterballoon launchers.
Eons ago, when I got FS1, I thought it would be a jolly good idea to have a hostile Aten surrounded a couple of freighters against me in a Herc. Unshielded of course since even back then I thought shields were wussy, lame and cheating. So I got killed before even getting two shots off. So I thought bummer and fitted shields on my Herc. This time I got off three shots and a couple of hasty evasions before getting killed.
Thank you, Prophet. Please have a big cookie. I've been thinking about this very issue lately, and you hit the nail right on the head.
The seeming vulnerability of capitol ships is indeed a result of the development of shield technology. If you've ever noticed, when you attack a capship you can usually expect to take one or two turret hits, but no more then that, as their travel speed and rate of fire are abysmal. They're very powerful, but they can't chew through your shields fast enough to do anything.
When you don't
have shields, then one or two hits is
enough. You're taking weapons designed to be effective against capitol ships right in the face, and you're in a fighter. That hurts. Remember that early FS1 mission where you have to attack a Vasudan supply depot? Those freighters are
brutal. The development of shields changed the fighter/capship dynamic considerably, and that led to the development of the previously un-needed flak cannon. I think that's as good a canonical retcon as any, hmm? It's also a good canon excuse for the fact that the GTA's only bomber at the start of the Great War was the Athena, which was light and maneuverable enough to weave through capship defenses. (IMO, the GTA having no bombers besides that at the start is probably a game balance issue, where the dynamics of the game demand that you slowly introduce new ships and weapons as you progress in the game, but this is a good in-story excuse that makes perfect sense.)
As for the usefulness of Cruisers at all- in real life, cruisers are big ships, that have nearly as much firepower as a battleship, but have less armor and are faster. They're used as fast-attack vessels that can do commerce raiding, and are capable of outrunning and outmanuvering heavier enemy ships while still packing a lot of firepower. That very much describes FS Cruisers mission role, although they're closer to real life destroyers, in my opinion. (Corvettes in FS2 are really "Cruisers," and "Destroyers" should be called "battleships.") The problem with FreeSpace is that you don't see enough of the supposed world, so instead of seeing all the things that Cruisers could be good for, it seems like they're only there to shoot at other Cruisers.
The point of a Cruiser is to kill enemy capital ships. In my opinion, this is a job it can do far better then fighters or bombers. It packs much better firepower then a fighter or even two wings of bombers, and it's better to have a heavily damaged cruiser and a dead enemy cruiser rather then two mostly destroyed wings of bombers (and their fighter escort,) and a dead enemy. They're heavy guns. Bombers? That's what your own fighters are for- escort.
Also take into account a few other features of Cruisers. First and foremost is cost. It's cheaper to build five Fenris cruisers then one massive Orion. The Orion can only be in one place at a time, your Cruisers can cover the area. Also, Cruisers are much more maneuverable in combat, and can bring their weapons to bear easier. That's even more important in the age of beam weaponry. This means they're useful in assaults on enemy Destroyers, because you can sneak them into a place where their small size makes them inaccessible to half or even three quarters of the enemy destroyers guns, whereas a larger ship would take the full brunt. They can also diesngange, if they need too. They're pretty cheap, and they can turn a close slugfest between two destroyers into an easy win for your forces. Not bad.
Then there's the matter of turret coverage. Cruisers are less vulnerable to fighter and bomber attack because they have all their firepower concentrated in one small area- if you're pointing your nose at the Cruiser, you're pointing your nose right at most of her guns, which gives them a low-deflection shot. Destroyers have their turrets spread out over their entire massive hull, which gives them worse coverage. I should note that even
with shields, a Fenris is a REAL pain to attack alone, or even with a few wingmen. Attacking cruisers with anything less then two wings to divide up it's turret fire is a real, real chore. Don't believe me? Go play the first mission of the user-made mini-campaign in Silent Threat, where you have to scan a hostile Fenris. Eeek. On the other hand, it's easy to take out a destroyer on your lonesome, if it doesn't have any fighter protection. Just bomb, run away to re-arm, rinse, repeat. Very easy.
Now there's one more thing to consider, and it's a big one- the mission role trade-off. The reason Terran Cruisers are so weak is because every weapon on their hull is designed to kick butt and take names on enemy capital ships, and it is indeed a terror in that role, but that leaves it with no effective anti-fighter weapons (except for the Leviathan, which has a single missile launcher.) Now contrast that with the SC Cain, which is a terror to attack in a fighter. Go pop into FRED1 and see what weapons the Cain is packing... that's right! They're Shivan Heavy Lasers, which is a powerful
fighter class weapon! They have a higher rate of fire and MUCH better velocity, which means they're great for swatting those pesky fighters and bombers. However, as everyone has noticed, this means that the Fenris, packing capital ship class weaponry, slays the Cain's face off. Fighter-class guns cannot compete with the power of capital ship class turrets. Hitting the target isn't an issue with Cruisers- it's all about raw power.
Now contrast the Lilith, or the Fenris. The Lilith has a hideously powerful array of capital ship turrets- it can tear any Terran cruiser apart and pose a serious problem to Destroyers in a fleet engagement. However, that means that enemy fighers can strafe it all day with little opposition (though the dual missile launchers on both Shivan cruisers give all their variants better fighter cover then the Terran ships.) That's the trade-off you make- anti-fighter, or anti-capship?
Wanna have some fun? Pop into FRED1 and load out a Fenris or a Leviathan with nothing but Banshees in every turret. Set three wings of Basalisks to come after it with Hornets, and see what happens. Heck, you can even set them to respawn infinitely and see how long the Fenris lasts. The Fenris will
school them handily. But now it's going to lose in a toe-to-toe with a Lilith, and is now the mere equal of a Cain.
You could easily introduce a specially modified "flak ship" variant of the Fenris or Leviathan for escort duty. If you want an example of a good use for cruisers, make a mission where you send them up against Shivan freighters- you know, those scary, scary freighters that have incredibly strong hulls and wicked turret protection? Yeah, commerce raiding is what a fast-attack cruiser like the Fenris was built for.
Well, that's just my personal over-analysis, for whatever it's worth.