Here are some of my rambling thoughts. Hope it sort of makes sence.
1, New Ship units: Fireships (Ancient age), Bombards (Medieval age), Sloop, Ship of the Line (Rennasence sp?), Monitor, Drednaught (Industrial Age), Heavy Cruiser (early Modern Age), Aegis Cruiser, Aegis Destroyer (Late Modern Age), Nuclear Attack Submarine, Nuclear Ballistic Missile Submarine
The Fireships are a fighting rowing ship that has a bonus vs Brimes, but cant transport units. Likewise, the Bombards have a bonus vs Caravels/Brimes but cant transport.
When you get up to the Rennasence age (sorry, I really cant spell that word) you have 4 Types of ships which then carry through the rest of the game...
a, Light Warship (Sloop-->Destroyer-->Aegis Destroyer)
b, Medium Warship (Frigate-->Heavy Cruiser--->Aegis Cruiser)
c, Heavy Warship (Ship of the Line--> Drednaught-->Battleship)
d, Troop Transporter (Galleon--> Transporter)
In the Late Industrial Age add in Monitors which are ships that get a penalty fighting other ships but a huge bonus bombarding shore positions.
Submarines upgrade like this:
Submarine--> Nuclear Attack Sub
" --> Nuclear BM Sub
Then you add in your aircraft carrier in the Early Modern Age, and that completes the ship classes.
Light Warships are used for scouting and escorting bigger warships. Destroyers get a bonus vs Subs and aircraft. Medium Warships are basically cheaper "heavy warships". Use them when you need naval power in a hurry but obviously they cant go toe to toe with real heavy Warships. Aegis cruisers should get a bonus vs aircraft. Heavy Warships are there to rule the seas and to bombard the shore with. They should get a penaly vs subs and naval aircraft. Submerines should get a bonus vs all other ships except destoyers. Nuclear Attack subs are just an upgraded sub, but can carry cruise missiles. NBM subs are subs with a very low detection chance (make them invisible to everything except nuclear subs, and then only a small chance of detection?) and are used with cruise missiles or SLBMs (see below) and are used with the much improved dipomacy screen in Warlords (yeah right!) to threaten AIs (or be threatened by the AI) ("If you don't give us 100gold tribute/robotics/dyes we may have to use our nuclear weapons located off your coast!").
2, New Air Units: Biplanes, Dive Bombers, Torpedo Bombers, Light Bombers, (rename current civ bombers as Heavy Bombers), Interceptors (piston engined and later jet engined), (rename Current civ "fighters" as Air Supperiority Fighters), Cruise missiles, Sub Launched Ballistic Missiles
These could upgrade something like this:
Biplane-->Dive Bomber -->Jet Naval strikecraft (e.g A6 Intruder)
" -->Torpedo Bomber --> " " "
" -->Air Supperiority Fighter --> Interceptor
" -->Light Bomber --> SuperSonic Jet Bomber (e.g. B1)
" -->Heavy Bomber --> Superheavy Jet bomber (e.g. B52)
Dive Bombers and Torpedo bombers (and later naval strikecraft) should get big bonus' vs ships but penalties vs Air supperiority fighters/interceptors. Dive bombers should also get a bonus when attacking ground targets. Light Bombers/supersonic bombers should have improved chances to evade interception. Heavy/superheavy bombers are more vulnerable to interception but are stonger and do more damage.
Cruise missiles and sub launched ballistic missiles are loaded onboard nuclear submarines. Cruise missiles are like a one shot bombing run which destoyes the missile but does loads of damage and cant be intercepted. SLBMs are like ICBMs but have a limited range (maybe twice that of a superheavy bomber?) and do less damage then an ICMB.
While Im on the subject, there should be a diplomatic penalty for using nuclear weapons from everyone, not just the person you nuked. AND THE AIs HAVE TO LEARN HOW TO USE THEM! ICBMs should need a building called a nuclear silo that they are based in (maybe a terrain improvement) that can be destroyed by enemy forces. This way you could launch a preemptive strike (either conventional or nuclear) to destroy another nations missile silos before they can be used... and this would make nuclear ballistic missile submerines useful as usually you dont know where they are until they fire their missiles.
3, New Wonders! As per Sevomod 2.9... Fairchild Republic Wonder lets the nation who builds it first build A10 Warthog unique Unit (A Strength 20 "fighter" with a 200% bonus vs tanks).
Lockheed Martin Wonder lets the nation who builds it first build F117 Nighthawks (almost impossibe to intercept against).
4, General gameplay improvements:
Planes can sink ships. Ships can bombard land units along the coast and destroy land terrain imrovements. The AI builds ICBMs and SLBMs and actually knows how to use them. Bringback those things from Civ 3 which defended cities from naval attack (shore forts or something). Get rid of sam infantry and replace with AAA unit (anti aircraft artillery). Air Supperiority Fighters and interceptors can perform an "escort mission" to protect bombers. All aircraft should be able to scramble to protect a city under attack (in otherwords they get to fight as defenders).