Honestly, I don’t really have a clear preference. As long as I like the story I probably will enjoy the visuals. Examples of one from each that I’ve enjoyed are: Rance, the modern visuals are clean and awesome. Radiant, I love the reflection on the girls skin and their models.
I like both if they're done right. Some 3D has a look that looks weird to me. Things like the character model is lit up more than the scenery. Or, the eyes looking more like glass beads than actual eyes. I've even seen where the mouth doesn't quite look right. In cases like that I prefer cartoon where I can just concentrate on the story instead of weird quirks in the models.
Having said all of that, I will admit that rendering can be hard. I've played around with some 3D programs. It's not easy. I tip my hat to anybody willing to stick with it.
Most of all, I like high-quality japanese/anime styled 2DCG. Then 3dcg, and least of all western cartoon. Although there are exceptions, such as Akabur