Gun Boat: Convoy Raider, Bomber, Screening Element (Gun Boats are a mix of the torpedo boats of WWII and specially armed and armored bombers flown during and after the Vietnam War, and for our purposes are really just superheavy bombers.)
Fighters should be able to take down Bombers and frieghters with little difficulty, and gunboats with some effort. However, destroyers, cruisers, battleships, and Carriers should swat them like flys.
Bombers and Gunboats should be able to take down freighters and destroyers with little difficulty, and cruisers with some effort.
Destroyers should be able to take down frieghters and fighters with little difficulty, and cruisers and carriers with some effort.
Cruisers should be able to take down frieghters, fighters, bombers, gunboats, and carriers with little difficulty, and battleships with some effort.
Battleships should swat freighters, fighters, bombers, gunboats, destroyers, and carriers right out of the sky. That said, Bombers, Gunboats, and Cruisers should be able to take them if massed and/or used properly.
Carriers are not really intended for direct combat. Thier power has always been in the small craft they carry. As such, most everything should have a good chance of destroying them, assuming the fighter and bomber screen is taken care of.
The biggest problem, and why it seems so unbalanced, is because there can only be two hundred people on at a time. In real battles, a battleship could stand off entire flotillas all on its own, and the designers have tried to be true to that. That means, a battleship and four fighters can stand off several times thier own number, especially with that silly four hour rule. There just aren't enough people to make the combat work like it should, so certain craft have to be made stronger and more versatile than they should be. This, of course, means the craft that are traditionally supposed to handle them quite easily, cannot. I have seen bombers take down lfs, hfs, vhfs, and gbs.
Now lets take a look at the frieghters and transports. They traditionally only had a couple of guns(if that), and those with just enough power to see off lf's and hf's in small numbers and singletons. That's why convoys were invented. Only rarely were freighters and transports given heavier armament.
How to help the situation? Make it so only house navies get battleships, cruisers, and carriers. Mercenaries, Police, and Bounty Hunters should be able to get anything up to a Cruiser. House Corporations shouldn't have anything bigger than gunboats, and few of those. For the unlawfuls, they should only have up to Gunboats with a few exceptions. I said before that only rarely were freighters and transports given heavier armament. Here is the rarely. Take a freighter, boosts it's shields, add more mounts, and presto-chango, you have a pirate cruiser. Now, make all unlawful craft slightly more powerful than lawful craft. This should balance out the cap ship advantage, especially if you decree that a faction can have no more than one battleship and two cruisers online at anygiven time. Multiple players could have them, but they would have to take turns playing them. That way we can have cap-ship battles with limited players and not have to munchkin smaller craft or throw out the four hour rule. As it is, everybody and thier grandmother has at least a gunboat tucked away somewhere. People should be saying, "Holy crud, did I just see an Outcast Cruiser!?!?!?", not, "Oh joy, three Corsiar Gunboats and two cruisers. Yes, you can has millions."
I know that what I described poses a substantial amount of work, but it will solve the problems we are having. Unlawful factions shouldn't have player battleships and carriers, even the unlawfuls fighting the house navies are fighting guerilla wars, not civil wars. House Corporations shouldn't have security forces with heavy ships, armies cost to much and they already pay taxes for protection from the navies and police.
Mercenaries an Bounty hunters traditionally have contacts into navy and police surplus, so an actual refurbished cruiser isn't out of the question, but it's certainly stretching it.
"Two things I know; Gravity sucks and Ion Storms blow. And that proves the universe is trying to kill us all" - Barren Waste, Captain of the Wasteland Wanderer
An approximation of my reaction when I see my next victim...er, these forums.