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I agree that ctypes is a bit more brittle - both ctypes and c extension modules can yield segfaults, but at least the c extension module is likely to give an error or warning when you rebuild it.
However, I'm getting the impression that:
1) In pypy, the C extension module layer isn't a complete emulation
2) In pypy, the C extension module is a bit disfavored compared to ctypes
3) In pypy, there's a performance expense for CPyExt compared to ctypes
3) (less important) In pypy, the C extension module layer is still too young to do much with at this time
I've been wondering if maybe there should be a way to check ctypes use against .h's at build time. That way, the brittleness should be about the same.