[IanOzsvald]

PyPy uses a modified Mark and Sweep garbage collector, CPython uses Reference Counting. C extensions such as NumPy (and so Pandas, sklearn etc) are compiled expecting Reference Counting. A translation layer is needed for memory management from PyPy to extensions like NumPy and that introduces overhead (historically - a lot of overhead).

[actionfromafar]

So, theoretically, all C extensions could be rewritten, too.