Ideally these sorts of "late-game disaster" should be the consequences of your actions built up over centuries.
Like, let's say you come out of the Black Death with a newly empowered peasantry that manages to win a whole bunch of
land rights that give them a lot of control over their land, but this consequently reduces the income (and satisfaction) of your nobility. You compensate with tax breaks for the nobility and make up the budget deficit with much more taxation against the peasantry.
Do that for a century or two, and now your peasantry is broke, bankrupt, landless (since they had to sell all their land to cover their debts), and having to work as sharecroppers just to do
something that can keep them alive. Let that stew for another century, and you have the French Revolution.
What if you
didn't side with the nobility, and keep your peasantry going as happy, relatively tax-free, and not beholden to landlords? Aside from your upset nobility, you might find your own state income significantly curtailed; one of the things often reflected in research over early modern economics is that these sorts of agricultural workers primarily start to innovate in the face of competition. A peasantry of sustenance farmers isn't gonna naturally channel into higher modes of agricultural production, and depending on their political power, the necessary "nudges" might become too politically unpalatable. Consequently, your country suffers from considerable stagnation while your nobility and burghers likely try to find ways around the empowered peasantry to build up their own wealth base.
The long-term consequences of your decisions should be what ultimately nudge you towards later-game disaster (especially in the face of the spread of institutions), and it might not necessarily be
possible to avoid this. Or at least, the necessarily political actions that you might need to take to do so could instigate civil war. Or they could weaken you against external foes, leaving you open for conquest. Or many other such roadblocks that only encourage you to push out reform until well after it being too late.
The late game of Project Caesar should be exactly when your chickens come home to roost.