It's a long and boring read, but here you go.
As in the actual complaints, as far as I remember, but this was a bit ago:
* our versions got rejected because they perform slower on CPython (while being faster on PyPy) and because they're 'unobvious'. At the same time, the C implementation of a lot of things there is very unobvious.
* we were not allowed to use array.array module, despite being in standard library.
* you can use gmp library for C, CPython, but not PyPy via ctypes
* C can use a bad random (that's fast, but also gives a really bad distribution), while PyPy not because Python comes with a random in stdlib
* custom malloc libraries for C are fine, tuning JIT parameters per-benchmark is not.
And various complaints like this. After some discussion, Isaac just kicked us out alltogether. Overall, my personal impression of the experience was that shootout is there to showcase things that are predetermined and we're trying to attack the status quo. This is obviously very personal, I don't have any actual data to back up this claim.