I think it is naive to think that a referendum on Lisbon would have decided the issue -
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I agree with this, however the issue is much deeper and reflects the inadequacies of both the EU and UK constitutions.
The UK constitution (or all the bits and pieces that are considered as one) does not require referenda to ratify international treaties, even those that fundamentally change it's democratic basis or sovereignty of the UK parliament.
The EU constitution treaty was an attempt to mash together various earlier treaties as the basis for the EU institutions - this was rejected in the countries that require referenda on international treaties. Then the changes it proposed were incorporated into the Lisbon treaty as a set of modifications to existing treaties, eventually accepted following some minor changes.
That treaties that change the constitution and sovereignty can be arranged and implemented without reference to the electorate must, imv, result in a democratic deficit - as eventually expressed in 2016.
If all EU (EEC) electorates had directly ratified the significant (constitution changing) treaties throughout we would now have a very different, much more democratic, EU. The fault is not directly that of the EU itself but of the governments and civil services of the member states. In our case, our own.