IMO, it's because in EUIII we had the bigger problem of the AI not being able to form coherent states at all. EUIV is a major improvement in that now we do frequently have a strong France, Spain, Ottomans, Russia, etc., whereas in EUIII these places often all became balkanized. So now that major problem #1 has been fixed, people are turning to major problem #2: the lack of internal management.
It's a difference, but that difference is entirely characterized by the absence of anything unique. CK and Victoria both have states that divide the map between them, but they also have much more than that. EU, on the other hand has an international system of states... and nothing else. The exception being trade,
which is very flawed but still a great addition to the game. I see it as a big step in the right direction.
I agree that CK and Victoria are better in that the states have more structure to them. But I think the "problem" is more fundamental than that. The way you deal with things within the state is very different from those without it.
For example, imagine you are the Ottomans, dealing with the Balkans. There are two challenges you are facing (never mind whether dealing with them is a challenge or not):
On the one hand, Serbia, which you want to conquer.
On the other hand, some people want to reform Albania, so there is some revolt risk.
Now, with Serbia, you can interact, and they will react to that. They might form alliances, recruit armies, theoretically they could/should just offer to be your vassal...
You can deal with the rebels as well: give in to their demands, suppress them etc. But all the action you do is from you. The outcome is predetermined. There's no AI, flawed as it is, behind the rebels.
I think the difference is that you can replace the Serbian AI with a player, but not the rebel one. And that's a fundamental difference. It's not necessarily BAD, but it is what makes development of the game different in those two areas.
BTW, of course you can play the vassal of another player in CK. But down at the province rebels, the same mechanics apply. For example, you can rule multiple provinces all by yourself. Which makes no sense at all, even in the modern world! Barack Obama simply CAN'T rule every person of the US personally! It's inconceivable that there's NOBODY between the ruler and literally everybody else.