No doubt you know the United States had a similar problem in their early days, and that nothing sufficed to resolve that conflict short of a half-decade of generally very ugly warfare. Here's hoping the "United States of Europe" so-called don't find themselves so afflicted.
From what I hear, though, that seems unlikely; it sounds as though those charged with its assembly are, whether or not they consider it in these terms, attempting wholly to preëmpt the democratic phase, by not only skipping straight to the bureaucratic sclerosis, but actually designing said bureaucracy instead of letting it simply grow in its own fashion.
It's an interesting idea, and probably the best chance they've got of avoiding the susceptibility to dangerous enthusiasms which is a young democracy's besetting flaw.
On the other hand, it seems at least plausible that attempting to subsume into federalism a range of distinct polities each of which has centuries of history as an independent state, without hammering them together by main force as was eventually done in the American case, is a project doomed to ignominious failure.
Whether it'll actually work and how well, I haven't the slightest, but I sure do look forward to finding out.