Yes, RedRooster has a good point.
Why is everyone so eager for a EUIII-like Holy Roman Empire? Don't you see that it's a decay version of the Ottonid empire? No player would like to play a set of decisions that would make his power base and capacities weaker and weaker until his authority becomes almost worthless.
I think that the HRE needs four basic things in CKII:
1 - The Pope has to crown the Emperor, and the subsequent Antipope and Antiking features. Which means that there can be a period with no Emperor.
2 - Conflict between the Pope and the Emperor. The Imperial crown should have special features regarding religion, and a series of decisions would allow the player to become Frederick Barbarossa and stand for your dominium over the Christian World and the Pope.
3 - Imperial Diets to elect the next Rex Romanorum. You could easily control them if you have a strong king and also wide support (or Pope's support), but if you don't... another one will be elected King of the Romans and will probably try to fight you, even though you're the Emperor.
4 - Decay. When the Emperor is weak, the HRE starts becoming more and more like EUIII HRE.
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Also, I never liked rebellions in CK. They were too weak. I mean, there can be weak rebellions, but when the Duke of Saxony and the Duke of Swabia rebell against the Emperor... God, they were usually crushed with little effort. Rebellions need to be something fearful.