hehe Agent roo, while your researching ships I think you should tkae a look at what those missles do. A cruise missle (in Civ III at least and the more lamen look at missle's. Cruise in the navy is determined by its guidence system and altitude of delivery) is defined as a guided ordinance that is a FaF (Fire and Forget) weapon launched from a platform (be it air or sea or land) at a surface target. Ship to ship missle's don't count which is what the Harpoon missle is. So thats out the door. ASROC and SM-2 are standard missles used for surface to air so those arn't cruise missle's either. the 5' guns are for sea to sea combat as well as shore bombardment. The phalanx system is a defensive only system used as a last measure to combat ship to ship missle's as well as incoming aircraft threats. Lastly the Mark48-50 torpedoes don't consist of platform to surface guided missles. So no, cruisers carry no tomahawk or AGM-86b cruise missle's, which today is standard issue besides the CALCM (Conventional Air Launched Cruise Missle) for the entire U.S. armed forces.
In my opinion I think its a bad idea to join the destroyer and guided missle destroyer class's into one. Destroyer's were originally your submarine hunters of WWII which also provided small fire support through 30mm HE MG (High explosive machine gun) and one 5" gun of more recent (their role has continued to be submersible defense). The Guided missle destroyer is the evolution of a new breed of ship. I believe it is very important to keep both present. One, because I think the destroyer must be represented in WWII combat as a submersible hunter (its main role in WWII), and two, because the guided missle destroyer doesn't have the same capabilities as most ships. It carries only missle ordinance and if ship to ship missle's have to be factored out since every (and I mean every, including attack and ballistic sub's) warship in today's Navy has them we can't well include them into attack and defense factors or every ship would be a cruiser (yes most ships are being outfitted with the phalanx system

). So in my opinion the modern naval power should consist of...
Modern Sea Power
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AEGIS Cruiser - Your main ship to ship attacker and defender
Guided Missle or GM Destroyer - For Air defense and cruise missle delivery.
Destroyer - Your sub hunter and finder
Modern Battleship - Your heavy fire support on the ground and sea, if you can afford it. Also carries one cruise missle.
Attack Sub - Your main undersea attacker with the capability to carry 1 cruise missle.
Ballistic sub - Your tactical nuke transport and delivery system.
Carrier - Your air support, weak in every other catagory.
I think yuor WWII sea power should look like this...
Industrial Sea Power
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Destroyer - Sub hunter, some fire support.
Submarine - Your underwater attacker.
Battleship - The queen of the seas

. Your bombarder and biggest attack rating of the industrial age at sea. AEGIS cruiser will change that around in modern times to signify the switch to cruisers as your main attack role.
Carrier - Air support.
You could include a cruiser but with all the modern untis it would be hard pressed to account for it. Plus it was a faster version of the destroyer with heavier guns and though it was important to the war efforts I think due to unit limit constraints it can be overlooked to give way for more accurate modern sea warfare.
I don't like the idea of completly factoring out the Battleship once more. It just doesn't make practical sense from a realistic stand point. We can produce them but we choose not due to constraints of warfare. What we have to do is make teh constraints of warfare make the Modern Battleship not nearly as viable a weapon as it was during the height of the industrial age.
Scenario
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You have say 10 Battleships during the industrial age, they consist of your greatest firepower at sea. Suddenly you can build a stronger more combat prepared unit with AEGIS Cruiser. The AI and yourself start pumping these out for the better attack and defense rate. At the same time the Modern Battleship becomes available making the Battleship obsolete and unable to be built. The Modern Battleship is faster but has a reduced attack, it can carry cruise missle's now but cost's a lot more to produce, and I mean ALOT. This is a deterernt, and even if you wanted to pump em out would it be worth it? not likely. So you continue on producing the newer, better ships with higher attack and defense rating such as the GM Destroyer or the AEGIS Cruiser which now provide the backbone of your Navy. Sure you may have some Battleships in service, but only a few due to the fact that their maintnence and cost of production is far to high.
Let us not forget that the battleship still plays a significant role in today's Navy in times of escalating conflict. We didn't recommision and upgrade them so they would look prettier

. They have a specialized task and objective that ONLY the Battleship can fulfill. But by making them so cost ineffecient to the scale of making them foolish for production then I think that will balance it out. You may be thinking, well what about the AI? Even if they do decide to push em out they'll be easy targets for your attack subs, Cruiser's, and GM Destroyers. Think of all the fun you could have watching a ship that takes 15 turns in modern times to produce in a city rich with shields sink in flames from a 4 turn Cruiser

. Realistic, I think so. Lets not forget to make the original battleship very Expensive to produce and maintain as well, we don't want 30 old battleships cruising around the world. Try and limit it so even if you did step up production everywhere the most you could turn out before the AEGIS is discovered is say 10 - 12 and their maintnence should be appaling. I think that would better represent the modern Navy and why we don't have the battleship in service to date.