What about introducing some very rare (probability cca 50 percent one will happen during a game) epic mega-events that would drastically change the game, but would also allow bored players and players, who like the "what if..." aspect of Civilization, to have some fun (even if in a bit drastic way) and challenge?
Because of huge impact of the following, they would have to be always optional (an additional checkbox when starting the game, possibly?).
I know, that many of the following can ruin the game eventually, but they can also make a great story...
I have things like this in mind:
Asteroid strike
Summary: A huge asteroid blasts a part of a continent off.
Text for pre-astronomy civs:
A star has fallen from Heaven near city of CITYNAME! There has been a terrifying thunder and flash, earth was shaking tremendously, burning stones and ashes were falling from sky and the waves have risen to bury coastal cities! Huge part of world is obliterated, the Sun herself has hidden her face, crops are dying. Is this the beginning of the end, or have Gods just punished the unworthy?
Text for astronomy civs until Space flight is discovered:
A huge asteroid has striken near city of CITYNAME. Millions have perished in a moment, more millions are expected to die because of earthquakes, famine and tsunami. Is this the end of civilization, are we to expect rapid descent to barbarism, or can we survive even such terrible catastrophe?
Text for civs with Space flight:
A huge asteroid has been detected on collision course with Earth. There is not enough time to divert it's flight nor destroy it, but we can expect it to fall close to city CITYNAME.
You have three turns to get ready for the impact.
(3 turns pass, then display text for astronomy civs.)
EFFECTS:
Area of effect depends on map size - larger map, larger effect.
Part of map (cca to swallow at least two cities if present) in circular shape is turned to ocean.
Large neighboring area is turned to desert, all improvements and non-mineral resources destroyed, cities lose 3/4 of population, 1/2 of buildings destroyed.
Cities in neighboring half of the world lose 1/2 population, a building is destroyed in each.
All plots produce -1

for 20 turns.
All ships in coastal tiles destroyed (tsunami is dangerous close to coast, not on open ocean).
A nuclear showdown
Requires at least two civs with nukes.
Text: Due to a technical error, our nukes have launched! Our communication channels with other world leaders have been already disrupted by first explosions, they are expected to reply in same way! It is time to move to the Vault, sir.
EFFECTS: All nukes of all civs automatically nuke cities of civs with with "Cautious" or worse diplomatic relations, if there are any. War is, of course, declared.
An Ice Age
Text - before Scientific Method: It is apparent, that summers are getting shorter. There have been sightings of icebergs in places they were never seen before. Animals are migrating frantically and the very direction of winds has changed. Is the eternal winter coming?
Text - after Scientific Method: It can be taken for granted, that our climate is changing drastically. Both our paleoclimate research and modern observation seem to prove, that we are entering a new Ice Age. We will not probably see the peek of it, but it is already affecting us and our distant grandsiblings will live in a much less hospitable world...
EFFECT: Climate gets colder, terrain slowly transforms in appropriate way - plains turn to tundra and ice, ice on sea expands... This event is a long-time one, because it takes several thousand years for an ice age to begin. Enough time to allow non-equatorial empires to get ready for their last-ditch attempt to grab some warmer lands before their resources get thin...
Some positive changes (deserts turning to plains..) in hotter areas may be also expected.
Next evolution stage
Text - pre-Genetics: A new race of man has arisen in the CHOSENCIV, their abilities unknown, but terrifying. They are like gods to us. But their acts speak for their humanity, both in bad and good. Will they be our nemesis or our saviors?
Text - Genetics: Some cumulative changes in human genome have found a great niche in modern world. It seems, that in a certain group of people, new recombination of genes has appeared and it grants them incredible fitness in terms of evolution. Bearers of these genes already know of their evolutional superiority and have easily taken control of CHOSENCIV empire. Are we going to be replaced like the Neanderthal people were?
EFFECT: Weakest civ gets it's difficulty level in terms of game effects lowered to Chieftain. Other civ's difficulty level is increased by 2. The Civ affected gets "barbarian bonus" also when fighting other civs.
Dormant nature awakened
kinda Heliconian stuff
Text - pre Ecology:
The stars have come to the right place, as suggested in ancient manuscripts and an age of plenty has come upon us! Seas are full of fish never seen before, woods are blooming with flowers! Has the Golden Age returned? This unexpected growth is destroying our fields, but if this is the paradise, then we will not need them!
Text - Ecology:
According to latest evidence, there seem to be long-time cycles in the ecology of our planet. These are bound to position of our planet and other bodies in our solar system. Various lifeforms have already adapted to these changes during past geologic periods, but our species is too young to have these changes hardcoded. We are entering some kind of a "blooming" period, a planetary spring. It can all look like a return of paradise, but who knows, what the future will bring, as new lifeforms and phenotypes hidden in genome of existing species for a long time seem to appear.
EFFECT:
100 percent more natural resources appear.
Woods grow 200 percent faster.
Each plot produces +1 food.
Time needed for workers to do anything is doubled.
Animals strength increased by 10.
Cca 25 percent of terrain turns to more favorable, but improvements perish in the process.
SETI success
requires Satellites
An alien civilization has been discovered. They are too far to communicate with us directly, but it is proven, that we are not alone. The societal impact is probably going to be huge. This inspires the whole humankind for new achievements in all spheres of public life, ranging from politics to science and culture.
EFFECT:
2 turns of anarchy for each civ for each religion present in it.
+5 relations worldwide
+50 percent research for all civs with Scientific method
+50 percent spaceship construction speed
+50 percent nuke construction speed (
Yes, we know, that humans are all brothers compared to the aliens. But we must also be ready to repel these alien bastards if needed, you know...)