If the graphics are good and the art style suits my tastes, I'm okay with either. But like many of you have mentioned, 2D is what most players are familiar with, and I think you all get what I mean when I say that sometimes having 2D characters is precisely THE whole point. Sometimes you don't want the realism/semi-realism; you specifically want anime-style ikemen because the whole escapism experience is just better when you don't start getting distracted by your LIs' pores when they inch closer to you, hahaha! To me, it's kind of like this: 2D otome games pull you into another fantasy world, while for 3D otome games it feels more like they bring the fantasy into the "real world" for you.
So basically I have a slight preference for 2D, but I do like 3D as well, as long as it's done well. Awkward animation/rendering can easily take me out of it.