Nukes are fine as they are.
By the time you get to the modern era, you're pretty much in end game. End game is supposed to be hard and the way nukes work, works.
I mean, if the big flashing icon telling you that someone has completed the Manhattan Project isn't enough to put you on your toes, then surely defending your borders a wise move anyway. Moreover, look at what your enemies have in terms of resources. the glowing green of uranium is hardly subtle.
If you don't have the tech to see uranium, then how do you expect to defend yourself against a nuclear weapon anyway. A couple of lousy fighters might shoot down the bomber, but it's carrying a nuclear bomb dude, when the plane goes down that bomb isn't teleported out!
Nuclear weapons work well, in my experience if I have the manhattan project and a few nukes on standby then other civs are less likely to attack me, why? Because a nuclear deterrent is exactly that.
If you attack a late game Civ who have nukes, then the chances are they'll send one in your direction, so take out their capability to do so. Pillage their uranium supply, get your borders sorted.
Nukes, IMO, pretty much raise the stakes of the game. You have to be more vigilant, you have to take a bit more responsibility for defending your people and you have to keep up with the arms race.
The way they currently work, is not entirely far off the reality of the 40's - 60's period where you either had them, or you were at risk.
Is it a pain when you get nuked, yes. Are there more than a few ways of ensuring that you're less at risk, yes. Should you be encouraged to just take some ownership of the situation and defend your civilisations people? Hell yes.
Just think of it this way, that little warning about the Manhattan project, coupled with the fact that the Civ in question have uranium basically means that you need your guard up because they now posess the capability to destroy your cities at will.
I've nuked and I've been nuked. And in my view, the only thing that needs changing is the scarcity of uranium!
Nuclear weapons, never leave home without one!
PS - Your poll questions are heinously one sided