In addition to being incompatible with (some) third-party libraries, pypy tends to use significantly more memory than cpython. It's also slower than cpython for scripts that don't run long enough to warm up the JIT, so you probably wouldn't want to use it by default. (Disclaimer: I'm basing this on experience with older versions of pypy and haven't verified it recently)
He memory thing is still an issue. I had to go thru. Lot of tuning on max GC size to keep it runnable for long times. Too low and it is slow and too high and it kills the box.
