Ok...firstly, I'm all for realism, but Nuclear Bombers on Patrol? 5% chances of Nuclear Vessels exploding? I have a feeling we're getting a bit over the top here.
What I do welcome is some revision of the nuke system. The idea of setting nukes with targets and when nuclear war erupts the whole game goes into a graphic mode so we can see the devestation being wrought would be an awesome display but I think a little impractical, it degnerates from Civ3s Turn-Based gameplay a little too much, I think most people are perfectly happy to give orders to units individual, watch them soar and explode and then get on with the next unit.
My main problem with ICBMS and tactical nukes is that they can't be destroyed. The whole balance of the cold war and nuclear warfare is about trying to destroy the enemy's nuclear weapons before they can be fired against you, but in Civ3 this is impossible!!! ICBMS and Nukes stay alive unless you attack them with a land unit then they are destroyed instantly. In my mod I've given both of them a defence value of 1 to at least let them get attacked by Bombers, but this still only happens when nothing else is in a square.
I assume that when ICBMs and Tactical Nukes are stored in Cities they are not in the urban area, but are indeed in Silos in the surrounding countryside. But I strongly feel that some kind of method of destroying them by bombers and other nukes should work.
Also, another thought. Frankly I firmly believe that nukes are not used enough. Just because the Cold War never erupted into a nuclear conlflict doesn't mean this was unlikely, indeed it is something of a miracle we never did have nuclear war. The massive damaging effect nukes have on your reputation simply make conventional warfare a far better option, you don't want to get your previous allies at war with you due to using nukes after all. I think the damage to reputation should be variable in the game dependant on how you use nukes. Using them as 'Battlefield nukes' that is, against enemy units rather than cities, should have a much lesser effect on reputation that using them against cities. And people who are at war with an enemy you drop nukes on, should only suffer a very slight reputation change from you dropping the weapons (imagine seeing Britain declare war on the US after they bombed Nagasaki!). Also I really think some smaller nuke effects should be possible, that just target one square, not one square and all adhacent squares , perhaps for the early Atomic Bombs and for small Tactical Nukes.