Jürgen Habermas, writing in der Speigel, understands the problem with the proposed changes in EU organization:

The failed referendums are a signal that the elitist mode of European unification is, thanks to its own success, reaching its limits. These limits can only be surmounted if the pro-European elites stop excusing themselves from the principle of representation and shed their fears of contact with the electorate.

This is the basic problem. You create a, “referendum over a treaty that is too complicated to be understood,” and when it fails, the solution is to eliminate the democratic element of the decision making.