To be honest, coalitions aren't all that bad... I simply think they pop out way too often. They should only form if you fight several wars in a row, having a continent wide coalition against you after taking a simple duchy is overdoing it.
Shattered retreat is destroys the pace of wars, but eh, I can live it.
The worst thing in the game so far for me are the rebellions to increase council authority. You can defeat all of your vassals 12 times in a row, and they can all love you, but they will always form that faction a month or so after their defeat if you release them, which forces you to throw all of them in jail, all the time, and be an all around tyrant, if you want to keep the council weak. Not only that, but should you lose a rebellion for increased council authority, be ready to have council authority be maximized in the space of a couple of years. You lose your +2 demesne, which means you are weaker than beforehand, and they can plan another rebellion right after winning the last one.
In my opinion, refusing a demand for increased council authority should result in a tyranny hit, not a goddamn rebellion, and there should be a cooldown before your vassals ask you for it again.