The details are open to debate, in the end we as citizens will have to agree on something. Personally I would not be opposed to keeping the national states as a form of federal states under the umbrella of a common federal government, but then again I could see a more prominent role for the European Committee of the Regions solving some serious issues.
I'm not a regionalist and not a nationalist, I don't care in principle if we break national states up into regions and those then reorganize, split or unify however they please and federate into a european state or if the existing national states federate as-is. And because I don't care I think the people who do care (like the various european seperatist movements) should be allowed to plead their case and make an argument about it.
Personally I am not affected enough by any of this to have a strong opinion and I suspect that, with a European Union that takes on many of the responsibilities and decisions that rest with national states right now, those movements to separate or unify would lose a lot of urgency. Just like (for example) the Troubles basically stopped when both the UK and Northern Ireland were part of the EU, without a rigid border between them.
I find the Europe of Regions conceptually fascinating, I'm just also worried that regionalist or nationalist tendencies could increase if we treat borders more like dividing lines between cultures, ethnicities, languages, religions or histories rather than imaginary lines on a map that only influence administrative divisions.
But I also understand that those things affect people and identity can be very caught up in it, so...
¯\_(ツ)_/¯ make a good case to abolish nations and have regions be the federal states instead and I'll listen.