What the EU lacks first and foremost is a proper constitution: a simple document that describes what the EU does and doesn't do, who does what, how, and under what conditions, and what the rights are it grants to its citizens and national governments. Since we don't have one, the EU can grow in any direction and in any way its architects desire. And that direction might not be what's best for Europe or its citizens, but for those running the show in Brussels. As Juncker once said: "When it becomes serious, you have to lie". And that is sort of what they did with the thing that is called the European constitution. It's a huge document and you have to be a legal expert to make any sense of it. And that too is by design: when several countries voted against the "constitution", they took out one part (making "An die Freude" the European anthem) and rewrote the rest in impenetrable legalese.
There are many good reasons for having *a* union. And there are many more for not having *this* one.