Lupin the Third: Fujiko Mine.
It is true though that over the years chara design changed, trending towards a more clean, minimal, "perfect-ified" or "doll-ified", style. I don't play JRPG, but in anime this "evolution" is evident to me, and from the little I see about newly JPRG, it carries over (it's natural afterall). I don't necessarily dislike the doll-like characters, though sometimes it is overdone (especially certain male designs) and I'd still like to see more not-embellished stuff (Fujiko Mine.. you too can see how different it is from the current generic anime aesthetic); but indeed they can frankly be a turn off.
Anime also is narratively becoming more self-referential, “too near to the fanbase” (I don't remember who said this), tropes more and more becoming staples or even cornerstones onto which build series*. While shortening the distance with the fanbase the distance with the others is widened. And I guess this too might carry over to JRPG, which would be another turn off element.
So maybe the whole extent of the "problem" is simply that JRPG and anime are too near: until they're bounded to animes (especially aesthetics) like they are, people will see them as “anime RPGs”. For people who already like anime stuff (and the aesthetics, and the tropes) this is fine or even a good thing, but for people who don't o just don't care, as soon as they get a whiff of that stuff presence in the game, they have little-to-no incentive in giving the game a chance.
(Maybe in the past having anime aesthetics was more accepted because the graphics detail was low and a gap remained: the games looked like having “japanese style drawn graphics", but they didn't convey the “this is an anime game” message that the detailed graphics now convey.. and if you add "doll designs" to that...).
I'm just pondering, please don't kill me.
* some people don't agree with this.