In particular, the build process is really painful (3+ hours on a high-end Xeon workstation) and quite immature.
I was particularly annoyed to discover that the build process isn't incremental -- if it fails for any reason, you get to start all over again.
The CPython extension support is also still very experimental (that is, if you have any Python extension modules written in C, be prepared for a lot of fun getting them to work).
PyPy also doesn't support anywhere near the number of OS platforms that Python does natively. It's very much a Linux, Mac, or Windows thing only. And it's heavily focused on x86 if you want to use the JIT version.