Running portage with pypy seems much faster than with python.

To enable pypy add the following to

sys-apps/portage build python_targets_pypy3 python_targets_pypy

app-portage/gemato python_targets_pypy3 python_targets_pypy
dev-python/pyblake2 python_targets_pypy
dev-python/bz2file python_targets_pypy

To set use of pypy system wide:

eselect python set pypy

As it seems the following is needed to really use pypy:

export EPYTHON=pypy