I would like a response to my specific points though about trouble the EU is running into

I would first like to have some solid evidence that these are caused by the confederal structure of the EU, and that they would be indeed solved by moving to a federal system. So far that seems to me like pure conjecture and also a huge gamble that could destroy the EU in the process.

That kind of abuse of power can happen under literally any system from fascist to socialist.

In a centralized state, yes. But that is exactly what a confederacy isn't. And the concrete example is that people in other states voted for Trump and thus directly interefered with the affairs of a state that didn't. That isn't at all comparable to a state internal problem.