People on the forum here and on other services have been discussing the alternatives to the 3D portraits. The arguments I've seen for alternatives are fair, and while I personally don't experience it, others have mentioned how the 3D portraits give an "uncanny valley" effect. And 3D portraits do have bonuses over the types seen in EU4, HOI4, and CK2; being that they are much more flexible in design, and if you want to show a lot of characters it's not practical to individually make 2D portraits for all of them without making repeats.
Another argument against 3D portraits is that portraits don't really belong in the game at all, but I believe it's been said that they can be toggled off, so I'm not really touching that.
I think the best approach for the portraits is to just put a "painterly" filter over it, so that it resembles a painting. Keeping it stylized would either solve, or diminish the uncanny valley effect; maintain the flexibility of the 3D model system; and look good (especially since the characters themselves are confined always to a relatively small section of the screen.
I am personally thinking of something similar to the animated trailers for CK3 and the art style seen there. Obviously what's in those trailers is probably much too taxing to incorporate into a game, but something of that sort would be skookum.
This is a bit longer than intended, but I tried to cover the bases. Probably missed some argument, but I think that it's unreasonable to just remove a system rather than iterate it for a different game.