When it comes to Supreme Commander, in most cases, equivalent units share equivalent functions and have a specific purpose--a purpose that the unit, being specifically designed for, excels at.
For instance, strategic bombers are specifically designed to drop a highly-deadly bomb that destroys most units caught inside the bombs radius. They excel at destroying buildings and ground units because they are specifically designed for this purpose. Maybe a strategic bomber has an anti-air weapon, but it's more of a "goodie". The anti-air weapon will not help the strategic bomber accomplish its task; nor will it help against air-superiority fighters, because air-superiority fighters also have a specific use they excel at--to destroy aircraft, and to do nothing but that.
Unfortunately, naval units have many "goodies" attached to them, as opposed to land and air units. (A goodie is an extra feature the unit has that can pose an advantage, but is not what the unit was specifically designed for. Usually, goodies do not help the unit to a great extent.) All these goodies can make it difficult to tell specifically what the naval unit is specifically designed for, so you could spend all your hard-earned resources building a specific unit trying to accomplish a specific task, only to find that you could have bought a cheaper unit(s) designed especially for what you wanted to do.
So this page is meant to describe what naval units are specifically designed for. It will not list "goodies." In other words, if one faction's submarine has torpedo defense, another faction's submarine has anti-air, and another faction's submarine has an exceptional shore bombardment weapon, these differences will not be listed--they are helpful, but there are units specifically designed with these things that are much better for the job.
Submarines/Submarine Hunters Edit
Submarines are designed as search and destroy vessel for above water vessels. They can only be attacked by torpedoes when underwater, so submarines are perfect for attacking naval units that are either poorly armed with torpedoes, or completely unarmed with torpedoes. Submarine hunters, as the name implies, are designed specifically as submarine hunter killers and as such are generally faster than the submarines. Do not be discouraged by the name though, although specifically designed as submarine hunters they are still adequate ship hunters due to their armament of torpedoes.
Frigates are early shore-bombardment ships, as well as early direct fire ships. Although they start losing usefulness when an opponent reaches T2, frigates are the most mass efficient anti-surface naval ship in the game, and it is encouraged to create massive fleets of them until an opponent has a UEF T3 Battlecruiser, which is highly effective against low health units.
Because frigates are direct fire units, they also help in attacking units that hover (which submarines cannot attack) and attacking other ships, as well as shore units in range of its weapons.
Attack Boat Edit
Cruisers are specifically designed as anti-air weapons, tactical missile defenses, and intelligence units. Their anti-air weapons are literally state-of-the-art, having a tremendous DPS and thus providing great anti-air defense for other naval units. In addition, their tactical missile defenses protect other naval vessels from being attacked by tactical missiles by surprise. And finally, Cruisers have the best radar of all naval units except for aircraft carriers, and the best sonar except for the Tempest.
With all that said, a cruiser is not an anti-naval vessel. However, if the need for AA defense arises, they are still versatile in terms of attacking shores
It should also be mentioned that both the Seraphim and UEF cruisers are equipped with tactical missiles, which are excellent for destroying static targets, such as point defenses, factories, or the occasional unfortunate unit. The usefulness of these missile launchers puts them far above "goodie" status, and are more of a perk for the UEF and Seraphim navies.
Additionally, the Cybran Cruiser has the exact same direct-fire armament as the Cybran Destroyer, making it a capable direct fire and bombardment unit far above "goodie" status.
Having direct fire weapons, torpedo defense and torpedo weapons, destroyers are specifically designed to attack other naval vessels, as well as provide bigger and better shore attacking. Except for the UEF Valiant, destroyers are excellent submarine killers, but the latter has the best single-shot damage for its guns to compensate. Besides, the UEF have a better surface craft for anti-sub work.
Aircraft Carriers Edit
Aircraft carriers are meant for holding, building, refueling, protecting and supporting aircraft. Although their anti-air weapons are not the best, they are decent enough to aid in the carrier's task of aiding aircraft.
Battleships have long range weapons with high DPS and a decent damage radius. However, battleships have a low rate of fire. Therefore, they are best for attacking high-priority targets, such as bases, groups of tech 3 units, experimental units, other battleships, etc. They are not very helpful in attacking low-priority targets such as frigates, tech 1 units and bases that units such as destroyers could take care of.
Battleships also provide further tactical missile defense to the fleet, as they are usually armed with two tactical missile defenses each.
Strategic Missile Submarine Edit
Strategic Missile Submarines are best for surprise attacks, since they can only build tactical missiles and strategic missiles. They are helpless against many naval vessels and are not the best choice for direct fire weaponry. But the fact that they build their missiles underwater increases the importance that these submarines are used for surprise attacks.
Missile Ship Edit
This is an Aeon T3 Missile Ship only. It is specifically designed for attacking major bases/high priority targets and overwhelming tactical missile defenses and shields. Lacking direct fire weaponry makes it a poor vessel for attacking other vessels.
In essence, it has almost the exact same purpose that a battleship has. However, it has a higher DPS than a battleship, and it has effective anti-torpedo weapons, unlike a battleship. On the flip-side, it costs more than a battleship and has less HP.
A UEF T3 Battlecruiser only. It is a support direct anti-naval ship. The Neptune Class has an impressive range, coupled with very accurate and high powered weapons, making it one of the most powerful ships effective DPS wise. They are somewhat expensive, but not as much as a Battleship. They have relatively low health though, and should not be put in direct confrontation, but rather, in the back lines. The best technique is to have several destroyers in your front lines to soak up damage, while your Battlecruiser take care of dishing out damage from behind.
They are much better than Battleships at support fire. They were not designed for shore bombardment, however. Their weapons do not have the range, and their laser aspect makes them very ineffective on un-even ground. For this task, build Battleships.