Beyond the Sword changed many things about the game, and naval warfare was one of the most dramatically affected. The limits on aircraft units per city changed the scope, but not the basis of air warfare. The additional units in land warfare made siege units relevant again.
But war at sea was completely changed.
In the vanilla CIV4, naval supremacy was nice to have but not necessary. The worst that could happen from not owning the oceans was losing some fishing boats and an air strike here and there (which you could counter with land-based aircraft). After your massed stealth bombers whittle them down, a few battleships can take down entire fleets of weakened enemy ships.
Cruise missiles and tactical nukes changed all that.
Now, not having sea superiority means that large stretches of your interior can be devastated, and possibly even nuked. The AI also uses amphibious assaults more often, and in conjunction with missle/nuke strikes. At the same time, the equation for gaining sea power has gotten more complicated.
A whole new naval strategy is needed.
To start, let's cover the main units.
Missile Cruiser
This is going to be your main combatant. Once onboard missles are exhausted, this is just a battleship and should be used accordingly. Promotions should be for Drill 1, Drill 2, and then Barrage. The idea is that you want the MC to survive initial combat, and then start prepping the rest of the enemy fleet for destruction.
You shouldn't feel the need to always have fully-loaded MC's, but rather keep a few empties around so that they can fight the battles. Once the enemy is down to ~27 strength, a Drill 2 MC should be sent in.
In a protracted war at sea, expect to build (and lose) a lot of MC's.
Stealth Destroyer
This is a misunderstood unit in because it's NOT a replacement for the destroyer the way a MC is a replacement for Battleship in every way. This is a brand new unit, like the Attack Submarine, and needs to be used in a brand new way.
Two basic role exists for Stealth Destroyers - surveillance and assassin.
In the surveillance role, the SD should have Flanking and Sentry to maximize the viewing radius. Surveillance SD's (S-SD) should be deployed to make EVERY ocean square between you and your enemy visible. There can be no fog of war when it comes to naval warfare unless you want an entire fleet to sneak up on you. The specifics of how such a picket line should be ployed will be discussed later.
Another use for the S-SD's is to sneak in and bombard enemy cities' cultural defenses, if your picket lines are close enough.
In the assassin role, the SD should have only Drill promotions, and hold those promotions in reserve for healing injuries. Once you kill opposing SD's, your highly damaged SD's can be in the middle of the ocean but also be perfectly safe. That's why your Assassin SD's (A-SD) should be the vehicle of choice for finishing off damaged units or hunting down tranports/subs/carriers. They're the only ones who can survive the aftermath.
SD's should emphatically NOT be employed in a stack with other units, the way the AI does. It doesn't buy you anything, since SD's won't defend against anything except another SD.
Attack Submarine
This is a critical unit, because the AI really loves to use submarines to deliver tactical nukes. Once you have Stealth Destroyers, you'll need Attack Subs in order to help locate and destroy enemy submarines.
Because Attack Subs should only be used against other subs or transports/carriers or heavily damaged units, it's in the same category as a S-SD and should get Flanking and Sentry. Additional promotions should be Navigation 1 and 2.
Submarine
This is also a crucial unit because it's the way to deliver tactical nukes and additional cruise missles to a front-deployed fleet. There's no combat role for the submarine because it's not powerful enough to fight any of the late-game opponents head on.
If you want missle strikes - better to deliver it from a MC, which can follow up with an attack or survive a counter-attack after getting close to enemy shores.
If you want to detect/kill other subs, the Attack Sub is much better.
That's why the main role of subs is to either shuttle cruise missles to re-load MC's which have fired their on-board supply or to sneak in a tactical nuke. As such, submarines receive Flanking and Navigation 1/2. Beyond that, add Sentry to help avoid threats.
Battleship
Whatever battleships you have as of the time that MC's come along - leave them alone. There's no need to spend money upgrading BB's when they don't gain any combat power and the supply of cruise missiles always tend to trail the number of MC's on hand.
Instead, use the BB's for the same role as they had in CIV4 original - escorting carriers and transports. Their MP's are perfect, once the transport/carrier has been upgraded with Navigation 1. They're just as powerful in defensive role as MC's.
There's no particular need to stock up on BB's, and also no reason to change how you use them from the original CIV4. You can't see SD's or subs sneaking up on you, but that's why you have surveillance SD's and Attack Subs anyways.
Destroyers
These are critical units which should be stockpiled in large numbers. Build them while you can and NEVER upgrade them. You can always build more SD's, but the supply of destroyers you have are finite
DD's have the ability to detect subs, they can move farther than the Attack Subs, and can kill the invading subs just as effectively. On top of that, they still retain their anti-air capabilities, so they're not nearly as vulnerable to air assault as the submarines.
DD's also come in the same 2 varieties as SD's - surveillance or attack. Unlike SD's, surveillance-type DD's should be used to escort large fleets because it'll provide some redundant sub-spotting (and killing) capability.
Otherwise, attack- and surveillance-DD's should be deployed near shorelines because they're so valuable and so vulnerable.
Carriers
In theory, carriers are much less useful than before. Air recon can't detect submarines or Stealth Destroyers, and the naval strike role which made Jet fighters valuable can now be taken over by missiles.
In reality, carriers are still useful for providing first-strike on detected submarines and MC's which have been stripped of their escorts. More importantly, they have a HUGE role in one of the main purposes of the navy - supporting a beachhead.
Forts
Technically not an unit, but so crucial it deserves its own mention. With BTS, fortifications act as cities for naval and air purposes. That means new tricks which were impossible before.
A naval unit can use a fort to create a land-bridge to cross an island while an enemy fleet must take the long way around. A ship can move from ocean-to-fort #1, then fort #1-to-city, then city-to-fort #2, and finally fort #2 to ocean. A crossing which might have used on the entire MP quota of a MC could instead be completed with only 4 MP's.
Ocean-Fort-City-Fort-Ocean
A fort can also be constructed to give you secure naval bases in stretches of your territory where it makes no sense to plant a city.
A fort can be used to house fighters/bombers to help support your coastal defense.
Now, if you're lucky enough to have an island off your shore, build a city on it just to be able to use it as forward air/naval station. Forts give you shortcuts to help chase down a faster enemy, and a secure way of bringing your transports further along before exposing them to attack.
But war at sea was completely changed.
In the vanilla CIV4, naval supremacy was nice to have but not necessary. The worst that could happen from not owning the oceans was losing some fishing boats and an air strike here and there (which you could counter with land-based aircraft). After your massed stealth bombers whittle them down, a few battleships can take down entire fleets of weakened enemy ships.
Cruise missiles and tactical nukes changed all that.
Now, not having sea superiority means that large stretches of your interior can be devastated, and possibly even nuked. The AI also uses amphibious assaults more often, and in conjunction with missle/nuke strikes. At the same time, the equation for gaining sea power has gotten more complicated.
A whole new naval strategy is needed.
To start, let's cover the main units.
Missile Cruiser
This is going to be your main combatant. Once onboard missles are exhausted, this is just a battleship and should be used accordingly. Promotions should be for Drill 1, Drill 2, and then Barrage. The idea is that you want the MC to survive initial combat, and then start prepping the rest of the enemy fleet for destruction.
You shouldn't feel the need to always have fully-loaded MC's, but rather keep a few empties around so that they can fight the battles. Once the enemy is down to ~27 strength, a Drill 2 MC should be sent in.
In a protracted war at sea, expect to build (and lose) a lot of MC's.
Stealth Destroyer
This is a misunderstood unit in because it's NOT a replacement for the destroyer the way a MC is a replacement for Battleship in every way. This is a brand new unit, like the Attack Submarine, and needs to be used in a brand new way.
Two basic role exists for Stealth Destroyers - surveillance and assassin.
In the surveillance role, the SD should have Flanking and Sentry to maximize the viewing radius. Surveillance SD's (S-SD) should be deployed to make EVERY ocean square between you and your enemy visible. There can be no fog of war when it comes to naval warfare unless you want an entire fleet to sneak up on you. The specifics of how such a picket line should be ployed will be discussed later.
Another use for the S-SD's is to sneak in and bombard enemy cities' cultural defenses, if your picket lines are close enough.
In the assassin role, the SD should have only Drill promotions, and hold those promotions in reserve for healing injuries. Once you kill opposing SD's, your highly damaged SD's can be in the middle of the ocean but also be perfectly safe. That's why your Assassin SD's (A-SD) should be the vehicle of choice for finishing off damaged units or hunting down tranports/subs/carriers. They're the only ones who can survive the aftermath.
SD's should emphatically NOT be employed in a stack with other units, the way the AI does. It doesn't buy you anything, since SD's won't defend against anything except another SD.
Attack Submarine
This is a critical unit, because the AI really loves to use submarines to deliver tactical nukes. Once you have Stealth Destroyers, you'll need Attack Subs in order to help locate and destroy enemy submarines.
Because Attack Subs should only be used against other subs or transports/carriers or heavily damaged units, it's in the same category as a S-SD and should get Flanking and Sentry. Additional promotions should be Navigation 1 and 2.
Submarine
This is also a crucial unit because it's the way to deliver tactical nukes and additional cruise missles to a front-deployed fleet. There's no combat role for the submarine because it's not powerful enough to fight any of the late-game opponents head on.
If you want missle strikes - better to deliver it from a MC, which can follow up with an attack or survive a counter-attack after getting close to enemy shores.
If you want to detect/kill other subs, the Attack Sub is much better.
That's why the main role of subs is to either shuttle cruise missles to re-load MC's which have fired their on-board supply or to sneak in a tactical nuke. As such, submarines receive Flanking and Navigation 1/2. Beyond that, add Sentry to help avoid threats.
Battleship
Whatever battleships you have as of the time that MC's come along - leave them alone. There's no need to spend money upgrading BB's when they don't gain any combat power and the supply of cruise missiles always tend to trail the number of MC's on hand.
Instead, use the BB's for the same role as they had in CIV4 original - escorting carriers and transports. Their MP's are perfect, once the transport/carrier has been upgraded with Navigation 1. They're just as powerful in defensive role as MC's.
There's no particular need to stock up on BB's, and also no reason to change how you use them from the original CIV4. You can't see SD's or subs sneaking up on you, but that's why you have surveillance SD's and Attack Subs anyways.
Destroyers
These are critical units which should be stockpiled in large numbers. Build them while you can and NEVER upgrade them. You can always build more SD's, but the supply of destroyers you have are finite
DD's have the ability to detect subs, they can move farther than the Attack Subs, and can kill the invading subs just as effectively. On top of that, they still retain their anti-air capabilities, so they're not nearly as vulnerable to air assault as the submarines.
DD's also come in the same 2 varieties as SD's - surveillance or attack. Unlike SD's, surveillance-type DD's should be used to escort large fleets because it'll provide some redundant sub-spotting (and killing) capability.
Otherwise, attack- and surveillance-DD's should be deployed near shorelines because they're so valuable and so vulnerable.
Carriers
In theory, carriers are much less useful than before. Air recon can't detect submarines or Stealth Destroyers, and the naval strike role which made Jet fighters valuable can now be taken over by missiles.
In reality, carriers are still useful for providing first-strike on detected submarines and MC's which have been stripped of their escorts. More importantly, they have a HUGE role in one of the main purposes of the navy - supporting a beachhead.
Forts
Technically not an unit, but so crucial it deserves its own mention. With BTS, fortifications act as cities for naval and air purposes. That means new tricks which were impossible before.
A naval unit can use a fort to create a land-bridge to cross an island while an enemy fleet must take the long way around. A ship can move from ocean-to-fort #1, then fort #1-to-city, then city-to-fort #2, and finally fort #2 to ocean. A crossing which might have used on the entire MP quota of a MC could instead be completed with only 4 MP's.
Ocean-Fort-City-Fort-Ocean
A fort can also be constructed to give you secure naval bases in stretches of your territory where it makes no sense to plant a city.
A fort can be used to house fighters/bombers to help support your coastal defense.
Now, if you're lucky enough to have an island off your shore, build a city on it just to be able to use it as forward air/naval station. Forts give you shortcuts to help chase down a faster enemy, and a secure way of bringing your transports further along before exposing them to attack.