The EU commission is voted in by the EU governments.
The EU council is made by the EU governments.
EU citizens elect MEPs.
There is no accountability because no one holds them to account and people repeat what you just wrote like gospel, including people writing for newspapers - and that has to stop.
You can pressure the EU as much as you can pressure your national government, all you need to do is put the pressure on your national government. Add your MEP on top, but the national governments are enough if you don't want to go the extra step.