The good 3d stuff can be really good, but often times I find 3d to be off-putting. I say that I prefer 2d more often, but the occasional 3d game ends up hitting right for me and I can keep going back to it.
When I started playing visual novels they were all 2D but over time I like 3D much more, one of the few that I still play is Summertime Saga, devs release the next update now, please
I like the art in 2D VN's but the back draw is most of the 2D VN's are made in Japan, so it is heavily censored. Which takes the kick out of playing it. And there are rarely any animated VN's for 2D.
That's the reason people prefer 3D in my opinion. I am personally a fan of VN's made using Koikatsu & Honey Select 2 Engine. They are unique and animated too.
if the work is animated i'd have to say 2d in general because they're usually better imo, sometimes 3d can lean into the uncanny valley or be stiff, whereas 2d feels more natural especially when it's hand animated. that said, 3d animations have gotten a lot better lately i must admit