In EU4 you can literally siege and occupy a whole country and eradicate every last soldier of the enemy army, and you only have a small fraction of the negotiation power to show for it, all so that the country can unrealistically bounce back in five years when the truce expires.
Lets stop and consider here what "occupying" a province really means, or at least is LIKELY to "mean."
First off we should note that many provinces in the game are enormous. Many probably include two to three major towns, if not two or more full fledged cities. This would also mean multiple castles or other fortifications, half-dozen or more villages, as well as agricultural, mining and foresting/hunting outposts. The forces involved in "sieging a province" can be as small as two thousand soldiers.
Obviously "occupying" a province does not mean, nah CANNOT mean, either (a) occupying all of the settlements and installations in the province, nor even (b) driving the enemy out of every one of them, much less (c) destroying all of them or (d) killing all of them.
These points are corroborated by the fact that, rebels fighting to liberate the province, can spontaneously spawn in a province that the player has "occupied."
In sum, you are taking things too literally if you think that "occupying" a province in game terms means that that province is completely and totally pacified, all possible combatants eliminated, all communities fully occupied and garrisoned, etc., etc.
What occupying a province is probably meant to mean is that one or perhaps two key strategic forts or perhaps towns have been besieged, causing some damage and death, and eventually the defenders of those settlements/installations surrender. The town in question likely still harbors would be rebels, to say nothing of all the other towns, castles, forts, etc. that any given province is likely to comprise. By taking control of one or two strategic points, the attacker has "occupied" the province, and can begin the process of garrisoning it enough to properly resist efforts to take it back.
To me, that reeks of a multiplayer-oriented balance decision, and it's really unfortunate.
"Reeks?" LOL bit over the top

Sheeze, so they make sure after they've designed the game that none of the elements are unbalanced in MP play.
Personally I think war (and specifically occupation of enemy territory) should be made a fair bit more expensive, but there shouldn't be any artificially restrictive mechanics that you keep you from conquering within your means.
Wouldn't necessarily disagree, and these are some things that mods can address.