I'm inclined to agree with OP, partially because I've been thinking about estates playing an internal balancing role for a while.
Pops going on in the background, away from interacting with the player, seems good because EU4's time lacks the all-important force of Mass Politics and consciousness.
The individual needs of your population don't really matter, because they have practically no voice and hardly any way to organize. Those who can organize, such as your clergy, your Janissaries, your nobility, burghers, etc. are the ones a king needs to take care of.
Now, the main idea in my mind is that Estates bridge the gap between CK2's character interaction and Victoria 2/3's POP interaction, and I'll use EU4 mechanics and terms for this.
First up, you would have "core" estates which make up your court and generally the people who make up your empire's bureaucracy: Nobility, Burghers, Clergy, Janissaries, etc. They don't represent provinces, but generally represent your main culture, your state religion, and traitorous snakes that want your crown. How you play determines their strength and interests. The nobility like conquest/glory and autonomy while hating the fact you allow burghers to continue existing. The clergy like pious actions, Holy Wars, donations, while hating the fact you allow heretics to continue existing. The burghers like money and development, while hating the fact you allow foreign traders to continue existing. They give powerful bonuses, but you'll have to declare a silent war against them to consolidate power. Upsetting too many of them will paralyze your nation.
Secondly, you would have minority estates. These represent all your non-state religion/culture groups in your states. For non-main cultures and religions it would be based on the majority culture, so no Catholic Irish vs. Protestant Irish vs. Sunni Irish vs. Hindu Irish vs. Shinto Irish. It would be majority (Catholic, probably) vs. your State Religion in the minority culture. Will you attempt to enforce your orthodoxy on these estates, taking time and money, or will you let sleeping dogs lie? Each culture can give a powerful bonus, but only if they're happy...
Thirdly, colonies. They generally just want more land, autonomy from your state religion/culture, and will become a live grenade in the Age of Revolutions. Oh well, at least you get paid.
Finally, the territories. I believe the best way is for any territory areas to be coalesced into a single estate based on trade zones. So you have a diverse set of people put under a single governor and now that hot mess is your problem, have fun. They have very questionable loyalty, and will need copious bribes to not attempt defection (in the form of revolt) to the nearest power of their religion/culture.
In broad strokes as France: You start with an illiterate majority populace, the nobility being the preeminent power in your nation, and the clergy being an albatross around your neck. Each "Age" should bring about a change to your nation, where the Age of Exploration has burghers upset the Nobility, the Reformation both forces you to tackle the Reformation and tackle the Clergy's influence over your nation, Absolutism would be where you (try to) sideline all your core estates, Revolutions would be where half your populace slowly realizes they don't have rights and will challenge your position as King.
Of course, this might be, in practice, a complete nightmare to play and even more to create. I'd like to hear any ways to improve on this idea.