It is representatives of the countries in the Council of the EU voting these legislations through: hold them accountable as you would hold them accountable locally.
Don't fall for the narration of the EU as a third party where your local representatives have no say. If four countries veto the bill, the bill is dead. 4 out if 27 - all done by influencing your government representative in the Council.
I don't think a central government for a single country is a good solution and I think an entity who can force countries to legiferate is even worse. Countries got pulled in into Europe because of the trading opportunities, not because they wanted a quasi-Federal Government.
We're witnessing a slow decline into dystopia and making the 0.1% richer and richer every day. VATMOSS and European regulations killed small business favouring Amazon. Covid lockdowns killed small business favouring Amazon.
I'm not sure whether the representatives are complete idiots who believe to the propaganda or who assume their voters are complete idiots (eg: I can't vote against protecting children, no matter what or people will think I'm a monster; I can't vote against massively complicating VAT laws or people will think I'm favouring Amazon) or malicious entities who just want more power in the hands of the government, but the net results has been always negative (not only in Europe).
I don't care how representation works in Europe or anywhere else, the facts speak for themselves: most governments end up behaving in ways that benefit big businesses.
Political activism is about making these "small issues" big and visible. It's not easy, it's not cheap and it doesn't always work. Yet it's something that can and should be done at the local level. And I really mean: local.
Your country's representative is of a political party that - I am guessing here - also runs in local elections. Your town, your province, your region - and that's how you start. You possibly can't talk to your ministers, but you can talk to your local politicians. Make sure they understand that their local power will see the consequences of national and EU politics, let them bubble up the issue.
Will it work for sure? Probably not, maybe yes. Is it better than taking ourselves out of the equation? Absolutely yes! Making sure that the local politicians understand that their national counterparts will affect their local success is a way of making them accountable.
Second, the issue is the presence of EU influence in my country: Whereas before joining the EU the local parliament would have a nuanced discussion and vote, often with results very different from partisan membership, now the party that won 4 years ago (that does NOT mean >50%) decides all by itself how it's going to vote in the council, and only the biggest issues of all can be helped, but breaking the government for every smaller thing is not feasible.
Individual countries are equally corrupted by big businesses and authoritarian leaning, but you can generally count on inefficient flip flopping right-left parties to not do too much damage in any direction.
The EU seems to be way more efficient in getting us straight to 1984 or Soviet Russia V2.