You are mistaken about Czech turnout though. It's the second lowest of all members: http://www.europarl.europa.eu/elections2014-results/en/turno...
[Edit] For comparison: Turnout in the 2014 US mid-term elections was 36%. In the most recent presidential elections it was 55%.
I suggest you read up on your EU constitutional law. The Commission is nominated by governments (and confirmed by MEPs); the Council is directly composed by national heads of state.
Commission and Council (i.e. national governments, all together) introduce legislation, which is then amended or rejected by the European Parliament (the body built with that election you mention). The first move is always from governments. In 99% of cases, when there is bad EU law, it's because governments wanted it.