Right now, both Nukes and Missiles are, strategically, pointless. They serve as either a two fingered salute on the way down after you've already lost the fight, or as a bling item. As a 22 city nation, I've been struck by 18 nuclear weapons and quite a few missiles this war, and I've really only just started to be modestly hamstrung by it because I've fallen below 25% of my starting infra. It is absolutely daft that I remain one of the greatest damage dealing members of my coalition, and not a radioactive wasteland. Here's my thoughts on what they could be instead.
New Nuclear Weapons, Suggestion A
Cost: 3 MAP, down from 12
Resistance Damage: 8-12, down from 25
Effects: Exactly as current, simply giving them a resistance damage and MAP cut so you can use more of them. Resistance damage to be set based on whether or not nuclear weapon use should be as effective as ground/air/navy for outright winning wars as fast as possible.
New Nuclear Weapons, Suggestion B
Cost: 12 MAP, as current
Resistance Damage: 25 MAP, as current
Effects: The city that is hit by a nuclear weapon should be totally out of commission. Somewhere between 70% and 100% of military units hosted in the city should be destroyed (roll a D31 and add 69). It should either 1; be completely unusable until the radioactive fallout has cleared, therefore providing no military capacity or resource production, or 2; see a much, much larger percentage of city improvements destroyed (we're talking half-ish).
Cost: 2 MAP, down from 8
Resistance Damage: 5, down from 18
Upkeep costs: Less
Daily purchase limit: Definitely more than just one.
Effects: Destroys targeted improvements by category the way it currently does, but with either no infra or only 50 infra (i.e. the amount of infra required for each improvement on your nation). Useful for chipping away at the military capacity of a nation, but won't win you the war in a straight race over ground/air/naval assaults. To be considered as an option vs nuclear weapons, they should also be very cheap to stockpile and stockpile at a rate of greater than 1 per day; perhaps they should require no Missile Launch Pad to purchase, but the Pad increases the daily purchase limit.