I think Blodir's post makes a lot of sense. Subs are way too vulnerable and generally seem underpowered compared to other naval units. Just look at their stats and how little they're used in high level games compared to other naval units.
Additionally, I think it's kind of ridiculous that properly micro'ed torp bombers are able to mass efficiently trade with cruisers, even though cruisers are supposed to be their navy-based counter. There should be at least 1 naval unit that can mass efficiently counter torpedo bombers (hover flak is not a naval unit, and 2 factions don't even have it).
Following the logic of Blodir's post, it would seem like adding more health and or torpedo defense to submarines and cruisers would improve the situation. Done correctly, submarines would then be viable enough to use more frequently without being overpowered, and cruisers could actually mass-efficiently trade with micro'ed torpedo bombers without being overpowered themselves.
Alternatively, there are other ways to address this issue, but they can get more extensive. For perspective, here is a quote regarding Equilibrium's navy balance: