To what extent does the European Union suffer from a democratic deficit?

French rejection of the EU, Brexit and Dutch Euro-scepticism are all example of the decline in support for the EU in continental Europe, which was formerly the unions biggest supporters. Arguably, one of the main reasons for this increasing euro-scepticism is the democratic deficit within the European Union. The EU is made up of 3 main institutions: European Parliament, European Commission and the European Council. Out of the three only one of the institutions is democratically elected, the European Parliament, thus emphasising the lack of democratic accountability the organisation has. In addition, the amount of powers and influence the Parliament has compared to the European Commission is much less as most of the agenda setting and finalising of policies comes from the Commission. Frequently this institutional body has been titled a gravy train in the media due to the large amount of Commissioners working and the lack of knowledge from the public as to who they are and what they are being payed for.
However, the European Union is set up so that European citizens are represented through their extensive involvement with pressure groups and lobbyists. The Council of Ministers is also an important body within the EU whereby each member states national leader will have direct involvement with policy passing through the institution. This is indirect democracy as the national people voted for their ministers to become involved in foreign affairs and thus have the mandate to work on public policy within the European Union. Despite the European Unions prominent role in the media, especially in contemporary politics, the institution does not have impact upon many salient issues such as taxation, defence, foreign affairs without the unanimous consent of all member states, and so involving the democratic leaders each states citizens voted for. These opposing arguments can showcase how despite the lack of voted members working for EU institutions checks and balances are still upheld alongside democratic values.