At the moment, it seems there are a few problems with naval balance.
First, torpedo defenses (T1 and T2) are rather underpowered, with T1 costing nearly double what a land-based PD does and doing less than half the damage.
Second, subs are odd. They do low damage and low health per cost, but because only destroyers/other subs can attack them, they are usually spammed for sea superiority. Also, battleships can hit subs with ground fire, which seems silly.
Third, strategic missile subs and carriers are about useless. They both have a purpose, but it's not as part of the fleet.
I hope to solve these problems with a few changes.
To tackle #1: All T1 and T2 torpedo defenses reduce mass cost by ~30%. So, that's going from 450 for a T1 torp defense to 300.
To take #2 is more complicated: First, all subs will get an increase in torpedo damage, about 30%, to increase lethality. Second, subs will float at a lower depth, making them less vulnerable to splash from battleships. Third, destroyers + UEF torpedo boat will be give greatly improved torpedo defenses so that destroyers strongly counter subs (now that battleships can't). Lastly, subs will be given sonar stealth when not moving and not firing, to give an element of maneuver/surprise to sub battles.
To solve problem #3, I'll modify all SMS/seraphim carrier missiles to be strong against T3 ships, but to miss against anything faster moving or smaller than them. I'll also make carriers auto-spawn torpedo bombers for free (including the Atlantis, when it is surfaced), but with a maximum of 5 at a time per carrier and a limited respawn rate (one every 20 seconds or so). (The torp bombers will not be controllable directly, rather controlled via a weapon on the Carriers.)
These changes, the greater of which were tested in the balance test mod, should greatly improve naval balance at all levels.