For the most part, either style works just fine for me.
If a game is going for the visual novel style, I do prefer 3D images and animations over cartoon styles, but cartoonish images aren't going to make me rage quit the game and bitch about 'the quality' unless the images look like they came out of MS Paint. Doesn't really matter what engine is being used, as long as it interests me and the graphics are not, eye gouging, low rez, junk.
I will add, that I do prefer cartoon style images in RPG Maker games. It is kind of an old school engine, so I tend to like the cartoon style, most of the RPGM games I saw with 3D in them, the images were a bit jarring. The images looked great, but just felt out of place compared to the default appearance of the RPGM interface.