The whole system needs an overhaul. Even in Vicky 1 where you had rebel divisions form (as unlikely as that is) they were easily put down for a number of reasons, chiefly- they suffered attrition which was much quicker than the time needed to declare independence for a region and/or switch alliegance to another power.
Some ideas to make rebellions more realistic-
1) Vicky1 rebellions never gave the real life sense that if you move troops from place X to Y then both places might rebel. This could do with looking at, It was too easy just to march a division from wherever to put down a rebellion.
2) The POP/region of the troops. Would they support the rebels if their home state rebels or they have similar issues to the revolters? Should perhaps be a factor methinks.
Conversly however, the HOI2 system, a simple partisan percentage did not feel right (and was quite dull) either and I dont think this sort of system would suit Vicky. A balance between the 2 needs to be struck or a whole new system.
National uprisings should be *real*, that is, they should create new nations at war with the parent state, with substantial armies etc. Guerilla uprisings can be modelled as events causing attrition to units in the province concerned and disorder and monetary loss to the national economy - fail to bring these under control for long enough and it should shift into civil war - either an independence movement in one part of the country or a war for control of the entire state. This would make these movements far more realistic, and more fun to suppress as you would be fighting a proper war rather than simply shuffling divisions.
Think of it like this - playing as the UK, for years you have been receiving reports of guerilla activity (i.e., a province modifier similar to the crime/corruption modifier in Vicky 1, but which also causes loses in military units stationed in the province concerned) in Ireland, but you have never been able to properly suppress it. Now you find yourself at war with Germany, you try to keep the lid on the whole Irish thing, but you have to draw down the number of troops in Ireland, gambling that nothing will happen there in the meantime. Your gamble doesn't pay off - Michael Collins, De Valera and the gang seize control of Dublin and declare an Irish Free State controlling large parts of the south of Ireland with its own government, flag, and army (say 4-5 scattered brigades). Now, you could make peace with them and recognise their state, but these are hard times, and anyway, you know that Ulster is on your side, so you siphon off some divisions from your front against Germany and crush the Irish rebels, forcing the surrender of the Irish. Ireland goes back to Guerilla war.
Now wouldn't that be much more fun than "You have lost control of Dublin to the rebels" occurring every few months for 20-30 years on end, shuffling a division in to crush the rebels, and then waiting for the next equally boring event?