How about tuning torpedo defence to be useful vs torp bombers?
I just did a little testing (replay). The UEF 'Stork' drop torpedoes that activate sub torp defences (usually only 1/2 torps hit). All other torp bombers bypass these (anti-torps don't even fire).
Further testing shows that 5 Storks reliably kills 1 Seraphim cruiser, but is less reliable vs 1 cruiser + subs. The subs sometimes block some torps from hitting the cruiser, sometimes don't (surprisingly the Aeon T2 subs appeared worse than Sera T1 subs).
All T2 subs and both Seraphim subs have torp defences. This allows the Sera T1 sub to sometimes survive the first pass from a Stork (400 HP, torp does 375 damage × 2).
What if this were adjusted and torp-bombers changed to behave like the UEF Stork (2 × real torpedoes) and sub anti-torps were re-balanced to more reliably counter the first torpedo? This improves subs vs torps and subs+cruisers vs torps, but not too much, and probably doesn't affect much else. (Maybe destro anti-torps should be tweaked to not block dropped torps, don't know.)