First and foremost, the game should be balanced so as no one faction has a direct advantage over any other faction (no rock paper scissor mechanics between factions). A players ability to win should be a direct reflection of his competence as a commander (just getting that^ out of the way)
This is a tough question because it has a lot to do with our perception of what the functions and behaviors of an individual unit should be. Regardless, I think that the backbone of any fleet should be the frigate class. Beyond that, I believe Balance has to do with fleet organization and ship design. I’ll try to give examples.
Disclaimer: Much of what I believe has been influenced by tank combat with regards to armor and shell caliber size.
Kushan Multi Gun Corvette
It’s intended role is anti-fighter.
The placement of the weapons around the hull should allow the ship to acquire any target in a sphere around it.
The caliber or the weaponry should be small to reflect it’s pure anti-fighter role.
Finally, the armor should be even around all sides to reflect how it’s target(s) might attack from any side.
It should be a very well rounded and pure anti-fighter platform.
Taiidan Multi Gun Corvette
This ship exhibits a very different design.
All of the weapons are forward facing with slight ability to pivot.
Additionally, the weapons appear to be of a larger caliber and should do more damage.
Because the ship is required to face it’s target to fire, the armor should be distributed toward the front of the ship
Both Kushan and Taiidan Multi Gun Corvettes should perform as anti-fighter platforms, however the Kushan should be superior to the Taiidan for anti-fighter, while the Taiidan because of the greater frontal armor and larger caliber guns should be a superior makeshift anti-corvette platform
These ships are interesting because of their combat behavior (turning it’s side to the enemy) This goes against the normal tactic of facing the front of your ship toward the enemy for best protection.
Because of this behavior, the greatest amount of armor should be on the side. The symmetrical nature of the Hiig destroyer makes me think it has even armor on both sides while the Vayg destroyer is asymmetrical and so i think should have its side armor skewed to one side (prob the side the missiles face).
This would make destroyers good for protecting the flanks of fleets.
Hiig and Vayg BC (last Ex.)
The overall design of these ships armaments aside, are very similar (the ship of your choice it sideways compared to the other)
The most important thing these ships can add the the fleet besides raw firepower should be the subsystems you build on them. as large as there combat role it, they should have an equally important support role
The vastly different combat mechanics of these ships should differentiate how they function in there supper cap ship role. They compare in a similar fashion to the preveously mentioned Multi Gun Corvettes (Hiig to Kush & Vayg to Taii). The sphere of fire on the Hiig BC shows that it is expected and prepared to face an attack from any and all sides while the Vayg BC has to be facing its target, and to reflect that, it should have massive amounts of armor in the front. In practice you might use the Hiig BC as a countermeasure to a flanking maneuver, while the Vayg BC is the centerpiece of your fleet dealing substantial amounts of forward damage from behind your frigates.
The most important thing for balancing is the first thing I said. With that in mind ships should be balanced by there design and made for an intended role.
I hope the examples helped to make my opinion clear.