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I may be wrong, but I'm pretty sure I've seen a general consensus that the late game rebellions are because of the economy. It's especially true when it comes to Jacobins.

Jacobins are usually capitalists and such.
Capitalists have several times more needs than the average pop. So much so, that they usually cannot fulfill their needs.
Not being able to fulfill their needs makes them angry.
No food and other things means angry rebellious pops that don't actually want reforms. They want basic necessities. Unfortunately, no government/party can provide them with this, so they'll stay militant.

For other kinds of rebels, I wouldn't be surprised if it was also economic related. I've heard of basic good shortages that are still being worked out in mods. They fix one thing, a new problem pops up or another thing unexpected happens. You could end up with a good that's completely worthless if its not balanced right.

If mods can't fix it instantly, I wouldn't expect Paradox to do much better. Not to insult Paradox, but it's just hard to compete with free labor from around the world. :p

That is gameplay problem, you created to many capitalists.

Yes, capitalists are nice, give -3% input for every % of capitalists. But you need to remember, there income come from factories, so if you want to have 4% capitalists you need probably 50% Craftsman working in profitable factories.
Otherwise this capitalists would not have enough income.
you should keep capitalists population down to manageable level. If you got Jacobin capitalists rebells, the best solution is mass demotion,. squeeze them with 100% taxes, beat there revolt and demote them, until they have enough income even under 100% taxes!

I see one additional reason why I never have revolts in my game, I keep different population on manageable levels, watching what is going on with them.

Some times I think we play different game or something reading this board.. because imy experience with rebellions that I always manage to prevent them.
 
Wow, this thread is depressing but makes me glad I decided not to buy Vic2 on release. I used to buy every Paradox game faithfully but after the really poor release condition of HOI3, and the way they basically banned or put on permanent probation anyone who pointed out the fact that the game was in poor shape, I decided to stop buying Paradox games until after they'd been extensively patched or a "complete" version had been released. I almost broke down and bought Vic2 because I liked Vic1 so much but hearing the problems I am very happy I did not.