This is really my point: you can't really have a conversation like that via a referendum. Repeat referenda are not really an option as your results will be increasingly biased towards the people with the strongest feelings/motivations.
Furthermore, the EU more or less worked the same before the treaty, and this treaty didn't really change that. In that sense it was a rather poor way to voice the specific criticism that the democratic nature of the EU should be reformed. I actually agree with that! I just don't think the referenda's were meaningful. If anything, it was counter-productive as the amount of nonsense mixed in with the better arguments just makes the criticism easier to ignore, and people who "just say no all the time" are generally easy to ignore in the first place (voting "no" is not a constructive way to improve things).