Do you really think that it would happen any differently, without the EU? There simply would be international treaties, which are even more opaquely-discussed, with no democratic oversight whatsoever and no recourse (national justice courts typically have no jurisdiction over international agreements).

With the EU, the process is formalized, opened up for scrutiny at many levels (sure, they could be more, there are people working on that problem), and then everyone can have a say through the European Court of Justice process.

The fact of the matter is that we live in an increasingly globalized world, and we must find ways to live together without resorting to the traditional genocidal ways (which are now practically unsustainable - a serious war on the continent would produce hundreds of millions of casualties). Somewhere, the political sausage-making has to happen.