The problem with this is that these hacks will continue to be used against the EU even when trying to reform them: It's easy to argue against handing sovereignty to an organisation with such a baroque decision-making process.
A lot of effort has gone into transitioning more powers to the EU parliament, but ultimately, it will be impossible to get where the EU ought to be in terms of which organs have which powers without very difficult processes in most of the member states.
Deeply direct democracy is self-sustaining - people would agree to move over to a new system because it would give them more power than they have in the current parliamentary systems.
The problem as far as I see is the current political class (parliamentarians and people in the executive branch), which would lose power. And since this is who currently has the power, and it's always nearly impossible to make somebody give up power, that's the reason why this won't happen.
But Europe is in a state of crisis now, and maybe this crisis is great enough to motivate this class to move to a more open system.
If you think about it, the current indirect democracy (with parliaments and the electoral college etc) is a remnant of a time when a decision took days to travel through the whole land, and to be reasonably fast and decisive, you had to have them. Thanks to the internet, we could even go past such direct democracies like Switzerland and allow each citizen to vote at each bill, or if she didn't want to spend the time, leave that decision to a parliamentarian of her choosing, but with the option to take power again or give it to a different parliamentarian at any moment. Now that is true democracy. No back-hand deals, and no favoritisms anymore.
Switzerland was always an okay model of how to run a federation.
Ceding sovereignity always leads to less democracy and more central control, not the other way around.
The EU is starting to look a lot like a modern day Austria-Hungary, only bigger. We all know what happened to Austria-Hungary: WWI.
As it stands, the Treaty of Lisbon went about as far as it could in handing additional powers to the EU Parliament while triggering the minimal number of constitutional changes for member parliaments, and look at the circus that turned into. And that was first after the attempt at a constitution failed.
The centralisation you worry about already happened many years ago, and the sovereignty issue is now largely the blocker to devolving more that power to the EU parliament, and after the trouble getting the Treaty of Lisbon through there's little appetite to take another round anytime soon.
That Lisbon has given substantially sharpened teeth to Parliament has been demonstrated repeatedly, with both the Commission and Council of Ministers having been forced to backtrack or compromise in areas where they previously would have been able to do what they wanted.