Pypy is a drop-in replacement only for a pure Python codebase. Add C modules (which most big Python codebases use at some point), and the transition to pypy becomes a lot harder
Another issue, at least for me, is complexity. I have way more trust in the CPython codebase, written and inspected by hundreds of competent programmers over time, than in the complex code generation machinery behind pypy. I have found and fixed bugs in CPython, but if anything goes wrong when using pypy, I wouldn't even know how to start debugging it.