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Nationalism starts at 3% (not counting the Dutch here :D ) and decreases with 1 percent every 10 year. Nowt else u can do about it bar quash the rebellions or don't annex foreign provinces :D
 
If the provinces you are taking are "national provinces" (which show your flag on the diplomacy screen, and for which you have Casus Belli on the former owner) you will have no nationalism in them. Otherwise you just gotta live with it. :D
 
It varies a lot but some factors that may influence it:

Population in the province
Fort size in the province
Your total army size
Your army (land) tech level
Build capacity in the province (this is in turn related to taxation value, etc.)
 
Generally speaking, small-population provinces produce small rebel armies. Sometimes so small they can't even cover the fortress, let alone besiege it, so they immediately vanish. (Kind of like the Easter Rising in Dublin which lasted two minutes, because a mix-up over dates meant that the several thousand people intending to be involved didn't arrive till the next day. When they did arrive next day, it got serious. :D )
 
I would rather disagree, Heyesey, IMO land tax value has more to do with it. But there are some factors not included in province.csv, for example Danzig produce 60k rebel armies with population under 10k and tax value about 7
btw, just played game when i managed to turn Poland-Lithuania reformed
and i don't mean state religion by that but religions of all provinces.Took me almost forty years, lots of cash and blood. in time i even forgot why i'm slaughtering all those heretics.
kill them all, God will know his own :)