So your proposal is to remove the input from the individual state governments and make it entirely citizen led?
Wouldn't that make it a government and remove the sovereignty of the individual states?
Not saying thats a bad idea - its just the exact opposite of the usual "undemocratic" rhetoric.
The EU could be just a bunch of agreements between countries about commerce and freedom of movement. The EU could be a federation of states with proper institutions. What the EU should not be is a superstructure over member countries without proper democratic control. And this is what is now and going worst by the day.
If you are interested in a federation, you could have an American bicameral model, with the senate representing the countries interest (1).
The current path of the EU is, in my opinion, very worrisome. The important issues are decided in close doors. The Commission and the Council feel that they can 'sanction' citizens without judicial supervision. The countries that not play along are blackmailed. The Commission officials feel that they can speak for all Europe when most citizens disagree with what they are saying. They feel that they can block the public discourse that they don't like, and now they want total control of our communications.
(1) - https://en.wikipedia.org/wiki/United_States_Congress