COOL FEATURES BELOW! So many new possibilities! Now subs can be usable units. Who will add these features?! This applies also for other civs.
Submarines should have special abilities:
a) be totally invisible for all other players units unless this other player research sonar. So you can track movement of enemy convoy and attack with other units (even by other players with shared vision). So you an check from where enemy is sending his convoys and prepare ambush
b) nuclear submarines should be able to swim swim under polar caps and stay there for X turns (e.g. 3 turns).
c) Submarines can carry one-man units (spies, diplomats, explorers, commando forces (yes add it!).
d) missiles should NOT be able to _LAND_ on submarines (nonsense), but misile can be launched from submarine.
e) submarines could refuel scout airplanes (yes, add scout airplanes - no attack/defense but great vision radius, can see submarines (with sonar), can be refueled by subs, long ranged, can have automatic patrol function). I mean these old WWII scout planes with land on water function.
f) subs can attack multiple times at turn (just send multiple torpedoes )
h) nuclear submarines can send torpedoes at 2 squares range, but attacking at longer range lowers attack value by 50% (harder to hit, bad torpedos). Such disadvantage should not be present for nuclear submarines (new topredo types).
i) when at WAR, coastal defenses (and fortified/sentry cannons and newer artillery units at fortresses) should attack nearby enemy units automatically. But not subs.
j) there should be "sonar" advance. Subs will be invisible for all units untill this advance. After this advance all sea units should be to see subs and attack it BUT Ironclad and older units should have lower detection range (one square max) and low power of attack on sub/defence against sub.
h) if sea transport unit contains one-person unit and it is sunk and nearby sub has free unit slots - there is 50% chance that nearby submarine rescue that unit. For rescuing enemy (or even friendly) spies/diplomats player can demand ransom
i) for cruisers and battleships subs will be visible in one square distance. For destroyers - two squares, for scout airplanes for three squares, for subs two squares.