Since Third Pillar affairs are intergovernmental agreements, publics have only one recourse...contact your local member of parliament and/or complain through national governmental channels. Pressure on national governments has the possibility to sway decisions by member states in third pillar areas. So there is a democratic channel for public participation; however, the problem is that these issues never get put before the publics in national political discourses. They are seen as technical issues.

As a long-time fan of the EP, I'd prefer to see most of these third pillar areas communitised into first pillar...but that isn't going to happen anytime soon.