I wrote up a guide to modern naval combat using BTS.
http://forums.civfanatics.com/showthread.php?t=243068
Even with the change to the Attack Sub, it's still true. Additional power to the AS is to just make it easier to nail other subs.
For example, your point about Stealth Destroyers are off-base
Stealth Destroyers are ideal for cleaning up because the #1 drawback for naval battles is that you use up MP's to attack and then a cruise missle counter-attack means your injured units are dead meat. Using Attack-configured SD's means you can wipe up the remnants and leave nothing for the enemy to assault unless the enemy also has lots of SD's.
Trying to counter every unit with itself is just a war of attrition with no strategy. Instead, look at the fact that the Subs have no air-defenses. Your goal is to detect the attack sub and direct air strikes against them. Then you can finish them with Stealth Destroyers which have comparable attack power but more mobility. Withdrawl is meaningless when the subs are being attacked.
On top of that, I don't expect the AI to use a lot of attack subs because they tend to prefer the normal subs due to the penchant for missiles and tactical nukes.
Land combat is better than sea combat because.
It promotes a combined arms approach, 1 unit type armies can be easily countered
The unit upgrades/promotions model enhances this further, because units can be upgraded with promotions to counter other specific units
Terrain plays a bigger role (not much you can do about this one at sea, as terrain type will never match land for variety)
A knight can be countered > pikemen > macemen > crossbowmen, and it goes on, the model is futher enhanced by the promotions system, that is also partly counter based, and finally planes/airships to this mix later on means there are a lot of variables an combat can go one way or the other based on a host of differant factors, which are unit types engaged, terrain, promotions chosen, available air power
Now look at naval combat
Does not promote a combined arms approach
Unit upgrades are all generic, more str, more FS, no enhancements to a units combat ability vs other units
Terrain inherantly offers less options for strategic postioning
The last point there's not much you can do about it but points 1 an 2 there are, i realise planes etc play a role, but planes should enhance the tactical model further not be the only way to break deadlocks, the sailing ship era is beautifully done
Privateers have special combat functions, but the lowest str
Frigates counters privateers
Ships of the line counter Frigates but are a little slower
Ironclads stomp the lot but are quite slow and coastline only
Simple system, encourages variety
10 ironclads might have the most muscle but at the huge expense of mobility
10 Ships of the line might be a good halfway house, but there slower speed means privateers with there 2 site radius will probably see you comming an outrun you
10 Frigates are pretty hard, but will be stomped if they run into a group of the above 2 an don't have enough moves to get the distance away needed
10 privateers are vurable to fast moving frigates
10 battleships won't be neutralised by anything bar another 10 battleships/MC, there's no counter, and thats were it's broken, outside things like airstikes etc have to break the deadlock, it makes for sameyness since with naval ultimately the best unit combo's are a sub or 2 for spotting a SD or 2 for spotting a loads of BS/MC to kill everything, thats why it's important to have a hard counter for every unit
SD may do a great clean up job like you say but only as long as i dont have them, so i cant counter you when i dont have them, an when i do they loose there advantage of invisability which is the reason you got them, so there two powerful when your the only one to have them an have no role when i do have them too, so they counter themselves
