I believe that now-a-days Religion is something extremely easy and you can, without any effort, survive and thrive through Protestant "revolution" and the Reformation.
I used to go straight for Humanist ideas with an continental European nation for that sweet religious unity bonus and -1 National Unrest I believe.
Now it's just a matter of having high legitimacy and little OE.
This applies to Religious Rebels and Nationalist/Independent Rebels... They are weak, at a certain part of late game, not even 50k Rebels are a problem, you have, at ease, 4 times as many troops and an obscene amount of manpower.
So I would also like to see real threats from Rebels, many stacks of them, to give even more randomness to the world.
Related to the topic, I agree, 100%