The main issue with your game may be that you've not given enough attention to your royal line...

The "whole faction goes rebel" thing in M2TW happens when there's no potential heir left to take the crown... It is one of the quickest and most effective ways of taking out an AI faction btw.

The fact that it happens around turn 100 also points in that direction : your starting monarch is generally about 40ish when game starts so should last about 40 game turns and his son should last the 40-50 next turns...

One way to avoid this problem is either by accepting adoption of generals, marrying your princesses to one of your generals or to an AI faction heir.

This should solve your problem.