Well as I said the historical aspect doesn't really matter to me, I mean it's an alternate universe with immortal leaders where history could progress in a much different way. so what if there are advanced ancient civs?
But YES, some sort of crisis that you HAVE to fight? that would be awesome, the current climate change mechanics don't feel like that much of a crisis. but there could be a million things, an epidemic, a barbarian horde, something to make the endgame a little more interesting.
Historical Aspect doesn't really matter?! Sacrilege! Abomination! Well, not really. It is, after all, a game only loosely based on history (damn loose, in places) and, of course, a completely historical game would be unplayable more than once because you'd know exactly what was going to happen every time just by reading a history book.
There are a whole bunch of Recurring Crises that have disastrously affected civilizations throughout history. They have largely been left out of the game because in many cases the Civ in question, in game terms, Lost The Game as a result, and nobody wants to play the kind of game where all your efforts can be wiped out by a 'random' event at almost any time in the game.
But to continue my original list, there are several things that could 'spice up' the End Game:
1. Climate Change, which is moderately modeled now, but doesn't begin to show the real effects, which are in the disruption of Food Sources in the form of fish yields and agriculture. A recent study has placed the cause of a great deal of the 'refugee' (read: Migration) crisis in parts of the world to lack of food back home. In fact, the original cause of the Syrian Civil War was farmers demonstrating because they could no longer make a living from their farms due to weather/climate change and resulting lack of production from their land. Add in those effects, and any game that lasted into the Information Era would present you with some
serious problems to solve instead of a few drowned coastal tiles.
2. Extend the game into the Near Future. Here we can take a page from the great but flawed game
Test of Time, a Civ variant that was full of really good ideas all very badly expressed in the game. One of them was 'near future' developments - extending the 'Future Tech' to specific technologies and their results. So, for example, Cities in Orbit (L5 Habitats), Cities under the Sea, Cities protected by 'Force Fields', Major Terra-Forming or Terrain Change (the game doesn't even reflect the current historical level of that!). Establishing a percentage of your total population off the planet, for instance, could be a victory condition instead of just sending a single vessel full of colonists.
3. The hoary old Trope of Science Fiction: Alien Invasion. Lions and Tigers and Lizards in Space Suits, Oh My! And, as above, some form of defense that can be cobbled together from existing or future technologies. Read Niven and Pournelle's classic SF novel
Footfall for an example of what could be done with this.
Crises that could be added all through the game, in addition to the Migrations and on-going Climate Change events (read Geoffrey Parker's
Global Crisis for the effects of Climate Change on Civs across the world in the 17th century CE: puts a whole new face on the various regime changes, wars, and upheavals from Mexico to China to England) would be the other subject that has been debated on these forums since the Black Death/Plague scenario came out: Plague.
Recurring epidemic episodes have had either catastrophic immediate effects (the Bubonic Plague outbreaks in Europe in the late Medieval Era) or on-going 'insidious' effects (the near-continuous Cholera outbreaks every single summer in most European cities up to the mid-19th century, when antisepsis and water purification were finally understood).
Again, they aren't in the regular game because if your Civ happens to be the one in the path of the Bubonic Plague in the 14th century CE, You Are Screwed by a random event, and, as said, nobody likes playing a game of Russian Civ Roulette.