What bugs me is the composition of rebel armies. I don't consider myself to be an expert for medieval European history, but how often did the knights and other soldiers rebel? Not very often, I think. And yet, the rebel armies in M2TW consist mainly of those troops.
On the other hand, there were a lot of peasant uprisings, and it would be realistic if the rebel armies are mostly peasants. Wouldn't it be nice when we would be confronted with a full stack of peasants, revolting against their feudal lords?

Another thing, when a city revolts, you just find your troops out of it, and a province lost. How did the rebels manage to do it? Did they, in the middle of the night, carry your sleeping soldiers and their beds outside the city walls??
I would like to have a chance to defend my city...

And when you look at the rebel army that now holds the city, you'll see that they are mostly high quality troops. When did they came from? If you can train only 3 units per turn, how can they train 20?