The self-determinism argument won't be compelling. Arguments that focus on structural problems rarely are. Pointing out that a system with structural problems has positive outcomes shifts the focus off the system.

For example, if there is a law which is overly broad and vague but the government currently only enforces it in extreme cases, (1) do you leave the law alone and trust in wise leadership, (2) do you redraft the law to be more narrow and specific, or (3) do you abolish the law? An argument which centers on evidence of good outcomes argues for the status quo and wise leadership. It isn't always a bad choice to leave some problems alone.

Still, the EU evolved out of an organization which represented nations and adapted itself to represent citizens more. There is a tension of purpose as the body changes and at the heart of its current structure. Is it an international organization or a federation?

Personally, I would have preferred to see Britain remain and engage in the hard work of reforming the EU into a more democratic institution even if that took a hundred years or more. I can't fault, however, those who don't have confidence in that project. I do look at the EUs legislative process where the Commission proposes legislation and am deeply unsettled. The strong representation of states in the legislative process by the Council and the Commission mean that it's essentially a treaty making body at this point. A criticism of that structure is important whether or not you favored leave or remain.