There always be some level of micromanagement, the point is how to make it fun. Here you would fight only one or two factions not a lot ( say in Otoomans case you would have Balkan freedom faction and Mamluk faction in Egypt/Arabia and perhaps orthodox faction), and only if you wouldn't persuade them to stay calm with some diplomacy options we currently don't really have. And it could even be the start of that internal politics game some people (including me) wants.Sorry, but this is just micromanagement again, isn't it? If you conquer a bunch of minor nations you just end up fighting a lot of small angry factions, which is just as annoying and time-consuming as fighting EU4's stupid rebels. Also, this only makes sense in Europe, where you have de-jure vassals. East Africa, SE Asia or in the steppes had vastly different administrative systems.
All I am saying is I don't want to conquer some area multiple times (the original enemy, first rebel wave, the second one, etc.). I want option to talk them out of it. I want to give Egyptian pasha something (tax autonomy or some tarrifs for example, I am sure Paradox could make up a ton of options) so he will shut up, and Serbians are weak so screw them. And if I have to or decide to fight, I want peace deal options that give me some profit, or white peace, or I let go something based on the warscore. And perhaps if I (or AI) screw up my empire will fall like the OP wanted.
Different administrative system don't really matter as they are not really modeled in the game anyway.