Things that vanilla game does better than mods?
Are there any aspects of the game where vanilla still beats what modders managed to make?
A lot of those things can be subjective, but I have an example - vanilla trees aren't very impressive (meshes were most likely optimized for consoles), but leaves and branches are fully animated to imitate reaction to the wind.
Many tree mods, even those with millions of downloads, actually downgrade (or perhaps sidegrade) the quality of the trees by removing branch animations. So while those modded trees look much better on static images, in game make things less dynamic. This is because tree animations is relatively new technology for modders, and afaik only Happy Little Trees, Ulvenwald, and Aspens Ablaze have animated branches.