It's true that scikit-learn was started and originally written mostly by PhD students (most were in fact CS PhDs), and the API they designed is amazing! A lot of the python ML ecosystem has adopted it and uses it - fit, predict, transform. I don't think any language has something comparable.

4 years ago they removed a misleading class - and even at the time the documentation was clear about what it was doing. I'm not sure how this reveals some huge flaw about scikit-learn. At best it shows that the contributors can realize their mistakes and solve them, without even needing people to point it out? That's great!

Also pointing to a bad implementation 4 years ago, for a project which has since then had way more funding for engineering time, and who's use has exploded, seems a bit misleading.