The Tidyverse is great, but vanilla R is a monstrosity. After five years of heavy use, I still don't really understand the random idiosyncracies of its various types. Arrays and lists and dataframes and tibbles are confusingly named, and operations that work on one type often balk at the others, without telling you what's wrong. I have lost many many nerves with it.

I agree that for statistics and data exploration R is certainly not clunky. My use case is more discrete PDE, where the R capabilities for sparse matrices and advanced linear algebra are a bit limited (but this may be just because I'm more used to the annoyances of numpy).