The EU leadership is the leaders of the 27 sovereign countries

Now you can argue there is a democratic deficit in those countries, sure.

There's democratic deficit in the whole system as this issue wasn't part of most internal election campaigns, effectively circumventing democratic process, due to lack of input from citizens themselves.

EU severely lacks checks and balances if it tries to be something more than trade union.

Are you suggesting the existence democracies that only ever implement policies that were a significantly theme during elections?