The biggest issue has been that CPython exposes its internals to native libraries, thus since many Python libraries are actually thin bindings to native libraries, this reduces the interest in using PyPy.

There is now new ABI proposal that should work across Python implementations, proposed by PyPy, but the uptake seems slow.

https://discuss.python.org/t/c-api-working-group-and-plan-to...

https://doc.pypy.org/en/latest/extending.html

With a good enough JIT, the amount of native libraries wouldn't be needed to the extent it is..