A lot of Freelancer mods try to incorporate capital ships into regular play. Obviously, Freelancer was never intended to have flyable capital ships. Because of this, it is very difficult to implement capital ships in a manner that is both natural and balanced.
Each mod takes a different approach to capital ships. Some go for the “realistic” route, where the bigger the ship the more armor and guns it has. Others try to give the ships specific roles and make them specialized.
In terms of creating a mod that is overall balanced, and not dominated by any one ship, the latter option is the only option.
If you make the ships better the bigger they get (which is fairly realistic), then I can guarantee you that the entire game will turn into one huge capital ship brawl when it comes down to competitive combat, with the victor being decided by who has bigger ships. Many mods try to balance this out by making the ships expensive, but this is never a solution. Cost will only delay the inevitable, not restrict capital ships.
If I were making a mod, I want the entire game to be balanced with itself in such a way that fighter pilots don’t become obsolete, and capital ships don’t become the be-all end-all to the game that realistically they would be. It’s all about roles. Every ship class must have a specified role and purpose, and you cannot keep the fighter world separated from the capital world. They exist in the same game, and they must also be balanced against each other.
For practical application, this is what I would do for capital ships. I am using generic names because I really don’t care what you want to call the classes, its just a name.
Light Fighters - These guys are the air superiority, they are best at killing fighters, but are useless against capitals, and also likely too quick to be hit by most capitals as well.
Fighters - These are all around ships. They have no real specialty, but they are decent at performing both the anti-capital and anti-fighter role. Jack of all trades, master of none.
Bombers - These are dedicated anti-capital ships. When a capital ship needs to go down, this is what you send in. However it must be careful of anti-fighter capitals and fighters.
Anti-Fighter - Small capital specifically designed for killing fighters. Decent armor, but stands no chance against capital ships with anti-capital weaponry.
Light Anti-Capital - Small capital specifically designed for taking out capital ships. Have awful fighter defense, a couple bombers could knock one out easy. However they are the best capital-ship solution for taking out other small capitals.
General Purpose - Small capital equivalent to the Fighter. It is not specifically good at one particular thing, rather it is decent at all roles. A specialized capital would perform far better, but lack versatility of the General Purpose.
Heavy Anti-Capital - Large capital ship with incredibly thick armor. Almost entirely devoid of fighter defense. However it will steamroll any other capital ship that comes its way.
Fighter - Counters are light fighter, anti fighter small capital, general purpose small capital.
General Purpose Small Capital - Counters are light anti capital, heavy anti-capital, bombers to some extent.
Heavy Anti-Capital - Counters are heavy anti-capital and bombers. Bombers can easily kill a heavy anti-capital as it lacks a reliable anti-fighter defense.
With the above setup, the entire game as a whole is balanced. Each ship has a role, purpose, and at least two counters. You must be tactical with your fleet composition and attacks. You need to assign priority targets to create a weakness in their fleet, and then exploit it.
This also creates a meta-game. A game outside of the game itself. Outside of how you will tactically perform in battles, you must consider strategically what your opponent is going to field, and then field counters to his fleet.
Using something like this, the ideal, general purpose fleet will be a balanced mixed of Fighter class, Small Capital class, and Large Capital class. Each class and subclass has specific roles and weaknesses that must be complemented by ships of other classes.
I went back and forth with another Freeworlds developer on this, as he tried to produce fleets that would be uncounterable, and initially, I thought he had produced the dreaded broken fleet. However when I sat down and thought about it, every fleet has a counter. The more you try to emphasize one or two of the class types, the bigger a weakness you are creating for yourself. In the end, the only way to create a fleet that does not have an exploitable weakness, is to have one that is thoroughly balanced with all class types represented and supporting each other.