1, the Holy Roman Empire. Its just that those rebels are also countries in EU terms. But how many Major European powers were there? France, Poland-Lithuania, Britain, Russia, Spain, Ottoman Empire, Austra/HRE. So That's 1 out of 8. If you lessen the 'small principalities' bit then you have Portugal and the United Provinces breaking free from Habsburg Spain.
But that's still irrelevant to the world conquest issue since the only real world European power that came close to a EU3 blob was Charles V's Austria-Spain union that split between family members because one ruler couldn't rule it effectively because it was too big.
Er, no. First off, the HRE was a collection of principalities for the entire period, it didn't suffer some grand, EU3 style collapse.
Second, historically sized Great Britain in EU3 can easily collapse into five or so states after one bad war, so saying no one historically got big enough is irrelevant.
Third, the Habsburg Empire was split because of it was too big to manage. Not because of rebels. So, how about making big states challenging to manage? Cuz "move army slider up, right click on province, move slider down" ain't challenging.
You've basically proved my point. This crap didn't happen in history, and stuff like the Dutch or Portuguese revolts don't happen in EU3 either. In EU3 there is no grand war of independence, there's rebels that pop up at regular intervals and get slaughtered until some war ties up the occupying country, and the player is close to immune to losing territory that way.
Really, though, history should be second to gameplay, and percent-based spawning rebel stacks have not been fun in any of the many games they've featured in. I've even been playing RTW again lately. That game has random little brigand stacks that pop up and will occupy watchtowers and stuff. It's not fun there either.