If Civ wanted to have 2 crises in the game, possibly 3, they could have integrated future nations into the crises. Let me explain;
The crises that happen at the end of each age have obvious implications based on their timing. The first crisis, out of Antiquity can be based on "barbarian" nomad nations-in-waiting attacking each nation. They would make sense to each Ancient civ's historical context. Egypt would encounter their Sea People (Vandals?), Rome their Teutons, Carthage their Berbers, China their Mongols, Maya their Aztecs, etc.
You could choose to surrender to these invaders and switch relatively peaceably, or you could battle it out to try to retain your original ancient civ, but possibly weaker after the battle. If the rebellion beat you, you would have your lands trashed, and be forced to switch.
The second crisis could include some modeled on peasant uprisings and reformation. Instead of proto-nations on your border, you could have some sort of internal rebellion, which could be religious or secular, proposing some new nation. You would again be able to agree to switch or fight it out.
The third crisis to a fourth age would be similar, except the rebels might brand you with either a Fascist or Communist ideology if you switched or fought and lost.
This would give players a choice on whether to switch, although peaceable transition would be implicitly rewarded by less damage to your lands. This alternative style of crisis would also have more interesting gameplay over time based on what nations would be in the game;
Instead of nation sets A interacting with each other --> B interacting with each other --> C interacting with each other
It would be A --> A OR B --> A OR B OR C
Maya --> Aztec or Maya --> Mexico or Aztec or Maya
Greece --> Byzantines or Greece --> Ottomans or Byzantine or Greece
Gauls --> Normans or Gauls --> France or Normans or Gauls
Inuit --> Danes or Inuit --> England or Danes or Inuit
... is this how your mod will work, Rhye?