There are some good ideas in this thread indeed. I do think that the 4th era's tech tree is rather lacking, and that nuclear-orientated developments would be one way of adding to it.
The concept of going into an Escalation Mode strikes me as a good idea, but I'm not sure it's practical or suitable for a game where each turn lasts a year (I'm strongly beginning to think that they should cut down the length of later turns to less than a year...) I agree that it might not fit well with the turn-based system, and it would prove just about impossible for PBEM games... I think that is something that, if considered, should be more of an addition than a main concept.
I do like the idea of the weapons impacting a turn after they are launched, and this would make sense were the turns not a year in length (see previous grumble). Also, this allows an extra year's use out of cities that should have been long-destroyed.
What I would propose for that is this: Whenever a player (or the AI) uses nuclear weapons, the first thing that happens on subsequent players'/AIs' turns is that they are given a warning about the attack. They are given all of the information that their current technology allows. This may be as little as "London's just been nuked! We have no idea who did it!" in the earlier stages, to "Korea has launched four Nukes at our cities of London, Hastings, York and Nottingham", perhaps with a list of launch co-ordinates and the actions taken by other players, when satellite technology has become more common. Before the usual pre-turn calculations are made (so before units are given back their movement points, and before cities contribute to construction and the economy, the player may respond by launching his own weapons. This means they may be able to evacuate some units to safety, and to deliver some nuclear weapons before they are destroyed. This could also depend on the technological level - before a certain point, players can only fire their weapons in such a crisis at predetermined co-ordinated (but they are allowed to choose which ones to fire, and which ones not to). After a certain point in the tech tree, the targets can be changed sufficiently quickly enough to allow the player to change targets at will, even during the crisis period. Nuclear Bombers would always be able to choose their own target, but of course they would have to be in range. Airlifts and rebase missions would be allowed as usual, but remember that we are still technically on the turn before, so not all units may have movement, and some airports may have already used their airlifts. After the crisis period is over, the incoming weapons deliver their blow, the turn is calculated, and the player may move whatever units survived as normal.
I do particularly like the idea of having a Nuclear Advisor (although I would make it an extension of the Military Advisor, but probably on a different screen), and the idea of setting pre-defined targets for each weapon. It might also be useful if the Military advisor could summarise known nuclear capabilities of other Civs, from whether or not they have completed the Manhattan Project (I think all Civs should have to do this), to known locations of Silos and reports of mobile launch sites. I think that the spy should be able to obtain such information, and satellites should be of use too, but I do not think that the Spy should be able to reveal every nuclear silo and mobile launcher in a single go; obviously, nuclear weapons must be kept separate from conventional weapons. This could be fun when you notice a nuclear sub just off of one of your cities, and you've no way of knowing whether or not it has a missile ready for launch or not...
Spies should be able to undertake (very risky) sabotage missions of nuclear silos and mobile launch sites - the success could range from being caught trying to detonate the device (very bad for world opinion), failing but escaping, sabotaging the device without the enemy knowing (when the try to launch it, it either detonates before launching or just doesn't move) or detonating it immediately.
One other change I would like to see is that all players should have to undertake the Manhattan Project (so make it a Small Wonder). Whilst you could argue that research of the technology should be enough, I believe this would fit in more with the way nuclear weapons have become placed throughout history.
I think that a good additional tech would be "NBC Survival" (Nuclear, Biological and Chemical - I think it may be referred to in some countries as CBR - Chemical, Biological and Radiological). Once discovered, all military units have an increased chance of survival against nuclear (or biological and chemical) weapons. The chance should still be quite slim - at Ground Zero, nothing would survive, but further away (yet still within the same tile, in game turns), units have an increased chance of survival, assuming they managed to equip themselves in time. Furthermore, this should make military buildings (Barracks, Civil Defence, perhaps along with Research Labs, Harbours and Airports, as well as airfield and fortress improvements) more resilient to nuclear attacks - not immune, but more likely to survive. For example, Barracks and Civil defence would be upgraded to make chance of destruction, say, 1 in 4, whilst the others listed could be 1 in 2 (tweak the numbers as you will). It should also allow the "NBC Shelter" to be built, which will reduce the losses suffered by a city's population.
I think that radiation from standard nuclear weapons should be made much harsher than it currently is, for example it gains the "disease" characteristic, similar to jungle but stronger - any units spending a turn (not just fortified) in a tile with radiation suffers a strong chance of being destroyed, or at least damaged. This amount would be decreased for military units, and for all units after the discovery of NBC survival. Heavily armoured units should receive less damage, and the risk should go down with time. Perhaps tiles with radiation convert to normal pollution after so many years. I think that radiation should also be made to affect sea and lake tiles - This could just revert to normal land after the radiation time expires, although I would rather see workers than can work water within city squares clean this up (I think there should be a tech, probably in the industrial era, that allows Workers to use ships to improve sea squares (within the city radius only), for example creating fisheries (extra food), offshore platforms (extra resources) or perhaps something like oyster farms (extra commerce). This would then also allow them to clean up radiation from sea squares). Long-term radiation should also completely prohibit any form of working the land effected, and the population of the city should be at risk of decreasing at a given rate due to the radiation (for example, each member of the population has a 20% chance of dying, or a 50% chance, decreasing by 5% every year, for example.) The centre square of the city should also suffer from radiation for the purposes of units (the city square is still productive, but units stationed within it experience similar effects to being in other radiation tiles (although the effect may be weaker, for example due to the use of fallout shelters.)
I do really like the idea of a robotic clean-up unit (in fact, robotic units in general that can safely pass through terrain containing radiation), and I especially like the idea of a fifth era for after a nuclear holocaust. However, the Civ franchise rarely delves into futuristic technology, generally sticking with what has been seen in real life. Therefore I doubt they would include these, even though they strike me as great ideas.
On that, I would have to say that some form of SDI defence would be a nice futuristic tech to include, in some way or another. I haven't actually experienced the CivIII version yet, so I can't really comment on it, but as far as futuristic techs go that seems to be one of the more obvious ones.
I would also like to see more use of things like satellites - with Silos and Missile Trains, the use of spy satellites in locating enemy nukes would be useful. Perhaps an additional Small Wonder, Satellite Network, would have, say, a 20% chance of spotting mobile nukes such as Missile Armour. They also have a certain chance of spotting Silos when they are placed. The Satellite Network wonder should ideally be located a fair while after the basic nuclear technology in the tech tree - this way, it's quite possible that the enemy may have already placed several silos before the Network went operational...
I think that WLTKD should not be allowed in cities that have been nuked for at least five years - in fact, I think that the first year or two, along with the year of the actual attack, should automatically be Civil Disorder. I think perhaps a good model would be that for a set period (for example, until the radiation disperses, although this would mean nothing for Enhanced Radiation weapons) all citizens that would usually be happy are only content, and citizens that are only content would be unhappy - this would make it VERY costly to keep the city out of civil disorder, and rightly so. Would-be unhappy citizens could either remain unhappy (making it very hard to keep the city in order), or could leave - they head for the countryside, defect, or kill themselves... My one concern here is that players could use the Specialist system to keep cities artificially happy. This can kind of be exploited already (when taking over enemy cities in the existing game), and would need a bit of a work-around.
Some ideas on the weapons themselves:
Modular Nuclear Weapons:
1) Warhead - Two types
2) Missile - Optional
3) Silo/transport - Ground-based silo, submarine, bomber, etc.
The idea is that a warhead may be built, and then combined, for example, with an ICBM or a Bomber, in order to be deployed.
Warheads:
1) Conventional (e.g. hydrogen)- A warhead designed to do mass damage to the area it affects (destruction of most buildings, population, units, and also forest/jungle and land improvements). Spreads radiation over a significant area for a long period of time.
2) Enhanced Radiation (e.g. neutron) - Designed to leave infrastructure intact, with radiation levels becoming bearable after days or weeks. In gameplay terms, mass damage to population and units, but no pollution and little damage to buildings and improvements. ER warheads would be further along the tech tree than Conventional warheads.
It may be worth considering adding biological weapons as a third type of warhead, with the same delivery methods.
Missiles:
1) SRBM - limited range, similar to CivIII's Tac Nuke. Can carry one warhead of any type.
2) ICBM - unlimited range. Can carry to six (for example) warheads of various types. Note that whilst the ICBM has an unlimited range, each warhead must be targeted at a tile within, for example, 6 squares of the ICBM's target. The ICBM itself is harmless, so would most likely be aimed at dead ground in the middle of a group of cities.
3) None - delivered by other means, such as Bombers or Spies.
Silos/transports:
1) Silo placed within building nation's territory, for ICBMs or SRBMs. Cost money to build and maintain, but dummies may be placed. Would be allowed in any square, regardless of improvements, but probably not cities. (Maybe not colonies, either). May contain multiple missiles (for example, up to four)
2) Missile Train - can be moved around the nation's territory each turn (but only on tracks, of course). Easier to locate (for example by satellite), but mobility offers protection. Suitable only for SRBMs. This idea could be accompanied or replaced by a mobile unit that travels on roads.
3) Bomber - existing Bombers (probably only Stealth Bombers, not original Bombers) can be given a warhead adapted for use as a bomb. This allows you to use the warhead with an existing unit, lowering the cost, and also makes it possible to launch without having the tech or resources for missiles (Just had a game with a technologically-advanced civ unable to nuke me for lack of aluminium! That said, there was no oil on the map either, so they couldn't have used a bomber either...) This would have the same range limits as that atype of aircraft normally has. However, when such a Bomber is set on Nuclear patrol, it becomes unable to perform conventional missions until the Nuclear orders are cancelled.
4) Submarines - you guys seem to know more about this than I do, so I'll leave it to you!
5) Satellite missile platforms - these would be very expensive, as you would need to build the warhead, the missile, and the launch platform. Depending on the level of technology when the platform is built, the missiles would either have pre-set targets, or could be changed quickly by the player by remote. The advantage of these is that they cannot be detected by enemy spy satellites, and that they cannot be sabotaged (although for the later, remote-control versions, it might just be possible for spies to gain the access codes...)
6) Spies - some people liked this in CivII, others didn't. Let's think of it as an option for now, which can easily be removed.
The idea of nuclear accidents happening sounds good to me, but I think the idea of 5% for each unit is a little extreme. How about a method like the existing Fission Plants - if Civil disorder occurs in a city where a nuclear warhead (not just missile or silo), nuclear (powered) sub, nuclear plant or nuclear-based spaceship component is being built or is stationed, there is a set chance that an accident will occur (for each such item in the city). This could also be extended to nuclear units or nuclear-powered subs within the city's radius. Also, if the civ's economy runs into debt, there is a certain chance that each warhead and nuclear sub could have an accident, wherever it is on the map. I also agree with the idea that nukes should be captured by units taking a city, but if they do not have the required basic tech there may be a chance the nuke will detonate.
Apologies for the length!