Haunters a good example imo. I think it's mostly due to the fact that the pixel art leaves a lot more up to interpretation (you have to picture the environment, how it acts, moves, etc.) whereas 3D is just like... yep... here he is... floating around all... sinister?
When you're bestest best bud doesn't wanna hang out with you in discord and listen to your dumb ramblings about kitty litter conspiracies and how wildberry poptarts are the best.