There's clearly a deficit of accountability though, regardless if you think the entire policy process here in intergovernmental. Member-states sort of know they can vote cynically at the EU level with their electorates not knowing much about it. There's a dilution of power that makes it impossible for electorates to properly hold their national and European governments to account.
True, the deficit of accountability is a genuine problem for the European Union and one of the reasons for Euro-skepticism but I don't think the problem is in the system itself but rather in a journalistic disinterest for EU-issues in many of the member states. I can obviously only speak for Sweden but the coverage here over EU-politics is laughably small compared to coverage and commentary about national politics. On paper both the council and the EP are accountable to voters since people can always vote out their national governments if they support EU policies that their electorate doesn't support, the trouble is that the electorate lack the essential information to actually hold either part accountable.
That isn't a problem that is solved by undermining national sovereignty though. At least voters sort of know what their own national governments stand for. When I vote for a party in the EP-election that belongs to the EPP will I get Merkel-style liberal pro-immigration euro-federalism or will I get extreamly conservative Orban-style authoritarianism?
It is easy to say that the Europe is union of independent states, if you have not to bother the reality. It is like saying that Sweden is federation of independent regions or the Reich was federation of independent princes. Obviously there are independence of states, but less than people like to think.
No it's not like saying that at all, because the Swedish government has its own army, a police force, an independent judicial system and its own separate international relations with other states, which the regions of Sweden does not... (although to be fair the Skåne Region had a try at the last one when they supported Copenhagen's bid to be the new location of the EMA against the will of the national government). Sure, as long as Sweden is part of the European union, EU-law is applicable here, but we're technically free to leave whenever we want (although it's hard, as the UK has showed). A region of Sweden can't leave Sweden unless the national government consent to it.
Sure the EU could turn into a United States of Europe, but that is not the way it is today and as I pointed out it's not what the voters of Europe want. As a matter of fact judging from Catalonia and Scotland they actually seem to want more sovereign states and not fewer.