I agree with the plague talk here. It's often very weird for the gameplay. It starts in some random place, lets say portugal. Over about 5 turns it spreads all over Europe. Your cities lose ~5 population and you might lose some units if you don't move them well (easily avoided in my opinion).
Overall it seems to do little to stunt the growth of armies but can be a good deterrent to large cities like an 18 population venezia. The problem I have is that it takes about 10 turns to do its deal (many less than previous versions), which is generally about 30 years. Didnt the plague take place over about 3 years or so? thats about 1 turn.
So if this would be possible (probably not, its likely one of those oh rhye did some intense programming magic that no one else can decipher), why not have it be so that when a city gets it, all cities within like a 15 tile radius will get plague and only for say 2 turns. If the plague starts in say iceland and no plague spreads then it will automatically spread to the closest city (to ensure it actually does something).
It could be that cities lose 20% of population (rounded down) per turn (for two turns). So a hugely urban city say a 21 population Paris would lose 4 population then another 3, droppings its population to 14 (exactly 33% which was the approximate population loss in european countries).
Cities under 5 population wouldn't lose population (the 20% rule and to prevent new cities from simply being driven into the ground).
Perhaps all ground units with 2 tiles of the city have a 80% chance to live per turn, so on average 64% survive (again about the 1/3 lost in the great plague).
Perhaps recently established civs could be exempt, say a new civ (within 10 turns) can't receive plague or start the plague (i doubt this will cause the plague from spreading, if it did then it would defer to the "closest" rule outlined earlier).