
For example, peasant households in Italy at the height of the empire had a wide variety of well-made pottery, some of it originating from production centers hundreds of miles away, along with tiled roofs; after the collapse, the variety and quality of pottery was greatly reduced, and tiled roofs disappear. (Tiled roofs provide better protection against rain, are less flammable, and require less maintenance and rebuilding than wooden shingles or thatch; but they also require large kilns, lots of clay and fuel, and a good transportation network.)
And ice cores from Greenland show extensive metalworking going on in Western Europe (in the form of copper and lead pollution carried through the air) during the Roman Empire; after the collapse of the Western Empire, the pollution levels don't return to Roman-era values until the 16th Century.
As for slavery, I object to how Civ makes it almost inevitable; at least back in Civ 4, you underperform for the whole game if you don't work your people to death in the Classical period. Disease definitely needs a larger part in the game as well...
I'd also argue for food insecurity and Malthusian limits (as in reaching the carrying capacity of an ecosystem -- or surpassing that carrying capacity, damaging the whole thing, and producing great mobs of the starving and desperate who'll eagerly listen to anyone who tells them who to kill to fix their problems) being conspicuous by their absence. Population growth wasn't all upside in the long ages that had neither the Haber process nor Norman Borlaug's hybrids...
But then, I've heard that an early version of Civ 1 tried to depict the rise and fall of civilizations, but players hated the fall part, so they just made it rise and rise. The mass market doesn't pay to feel uncomfortable...
[1] Ward-Perkins, Bryan. The Fall of Rome And the End of Civilization
[2] Brownworth, Lars. Lost to the West: The Forgotten Byzantine Empire That Rescued Western Civilization