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Ah see I got the the EU Commission and the EU council mixed up. Tx :)
Yes, things are so complex can't disagree. Voter turnout for the MEP election is usually a lot lower than for local elections.
It is already a problem in the UK where a lot of people are still uninformed about how the local system works (front benches? back benches? whips? FPTP/STV? Eh?) and there is definitely an added layer of complexity.
The EU did in the end move on CETA and TTIP due to protests/member states reaction to these.
The EU Commission is not elected, because it comprises civil servants, although the heads of the different departments are chosen by the Parliament. This in itself isn't hugely problematic, as most UK law is drafted by civil servants too, and EU laws need approval from the EP.
The Council of the EU comprises the relevant ministers, who are elected, and the EU Council (who chose these names!?) is made up of the heads of state.
The trouble is, the process of passing EU legislation is so unwieldy and long-winded that there are numerous shortcuts which are not particularly transparent or democratic.
I think the main democratic deficit in the EU is that people just don't really care or find it interesting. This means that proper scrutiny isn't really done, because no one really reports on or cares about the majority of what happens.
Then when the "unelected, bureaucratic" lines are used, people will readily believe them, because they don't care enough to know any better. It's hard to disagree, because even people who are ardent supporters of the EU dob t actually know what all its institutions are or do.