What I personally think we need......
---More nuke types: Small bombs(dropped by plane not missile), missiles, super-nukes, etc
---Retalliation Ability: (best way is to allow the all nations with nuclear technology the chance to see whats going on so all missiles based nukes can be launched and arrive at once) this could also allow plane based nukes to be cheaper, but not have this fast retalliation ability.
---Bunkers: for protecting population and or select unit, This would make nukes far more realistic for warfare instead of a "entertainment" option as was mentioned above.
---Non Tech Based Missile Defense: Instead of the classic SDI tech, At the very end of the tech-tree you could get very relaible anti-nuke units, that could shoot down any missile based nukes, but only in a very limited area, and they would have no affect on bomber launched nukes (you would need aircraft to take those down) Making nuclear warfare viable towards the end of the game as an actual way to win between to rivals (take out there nuclear defenses and blow them away)
---Nuclear Research Changes: All nations should have to Research there own nuclear programs, not one wonder getting them for everyone (very unrealistic, and takes away the "nuclear race" type thing in WWII).
---Plant Nuclear Device Spy Mission: This might be to touchy to include due to the current political climate. But once you get a very high level of nuclear weapons, you should be able to plant a "suitcase" nuke for a very high price in an opponents city.
---More interesting & Realistic Nuclear Effects: Both graphic and gameplay effect for nukes should be changed, there should be a unit destruction system whereby the percentage chance for a unit/building to be destroyed at different ranges is modified, as is the damage to city population and improvments, and where a city could be COMPLETELY destroyed. Tiny nuclear bombs doing minor population and low percentage unit damage in a single square, while super-nukes, would cover an area the size of a small continent, and obliterate 100% of everything in the very centre square with damage decreasing slowly at range. (maybe you could make some big nukes capable of also destroying bunkers, with direct hits as well)
---More Realistic Fallout And Radiation System: Fallout takes sometimes several turns to fall downwind, radiation disappears on its own over time, radiation has different intensities, leaving some sqaures uncrossible and uninhabitable for many turns after the original blast. Radiation should be different than pollution and should be capable of causing massed global "winter" some times only small cooling, somtimes causing huge amounts of squares to become frozen wasteland, in the years after a nuclear war.
---More Realistic Nuclear weapons use affect in diplomacy: Enemies should hate you, nations with bad opinions of you should get worse, nations with good opinions should remain the same unless you continue to nuke long after the enemies attacks have stoped, allies should stay the same, or even get better if it was an enemy you nuked, and best if it was retaliation against them for an attack on said ally. Also there opinion should be heavily modified by weither you have nukes or have used them before, i.e a smaller nation with no, or very few, nukes will never declare war on a huge opponent that has used nukes often and has many of them no matter how much they hate them.
---Better Use of nuclear weapons/defense by AI: AI should look at the diplomatic situation before retaliate, and some times might surrender (occupation feature) or offer you gifts of cities, anything they have to stem the nuclear slaughter

, also would effectivly use nuclear defense and base nuclear attack/retaliation one you and your allies nuclear defense and attack ability (like the AI will be unlikely to nuke if he knows you and you allies got defenses and he does not)
These are just a few easily implemented ideas that would make nuclear weapons more fun, more realistic, and more tactically useful (with bunkers/reliable defenses) especially in the late game.