I agree with the general sentiment that CK III handled 3D portraits better than Vicky III, but I still feel like even with mods improving the appearance of the models that they just aren't for me. It's just too much of a "cartoony" art style that I don't like to see in my Paradox grand strategy games which I associate more with realism. That doesn't mean that cartoon styles don't work in anything, I think they work in Civilization for example (though not VI, I really didn't like those ones personally) but not in a giant epic scale RTS nation builder that takes literal days in real life to finish like Paradox games.
I'm more accepting of the 3D portraits in a game such as CK III due to inherent focus on characters (personally I want an EU-style game during the Medieval period which sadly CK III moved away from that), however I still greatly preferred the 2D portraits of CK II. Now personally I don't even see the necessity of portraits in EU V, this is after all primarily a game about steering a nation through the transition of Medieval to Modern, I don't need a giant UI screen showing me a a 2D or 3D portrait of the king, just how he is doing as a ruler in an overall UI menu about the government or dynasty.
If we are going to have unique random 3D portraits for everyone, the monarch, chancellor, advisors, governors, and everyone's mothers, then the Imperator system of having a small window next to their name in the corresponding tabs showing a small portrait of them would be the best method, with obviously the quality of the models being improved. Basically just shifting EU IV style to 3D (advisers were the only portrait you saw and it was only in the court tab, 3 small windows, no full body shots) with a focus on keeping a more "realistic" style 3D (obviously I'm not asking or care for giant AAA uber realistic face model).
Portraits are nice in the games but they shouldn't be the selling point, Paradox shouldn't feel the need to have these big fancy 3D full screen models, keep them nice and small and fit the style and theme of the game. 2D portraits in my opinion are superior, but if the development team feels the need to move towards 3D than I definitely feel that the Imperator system would work best if improved upon.