media-gfx/pydot does not use any of the python bindings provided by media-gfx/graphviz (as it just calls the /usr/bin/dot executable directly), so it should not depend on graphviz providing bindings for a particular python version. Specifically, the "[${PYTHON_USEDEP}]" should be removed from the media-gfx/graphviz dependency in media-gfx/pydot.
Don't you have commit access? :P
ok thx for clear description, removed. 19 Jan 2015; Ian Delaney <idella4@gentoo.org> pydot-1.0.28-r2.ebuild: correction to dep graphviz, fixes Bug #537014