Why can't we just remove the Council and make the Commission answer to the parliament's legislative initiative? Well, for two reasons. First "we" the people of Europe are represented democratically by our national governments. They compose the Council which is very analogous to a Senate (think: German Bundesrat). But as far as the structures of the EU are concerned the people are not directly sovereign. Sovereignty is delegated in the National Governments. EU treaties are entered into, in our name, by Plenipotentiaries of the member states. So, unless and until European policy at the Council becomes the number one political issue in a national election campaign, there will be no real chance of reform.

"...through national elections" I want to add.

So, what other options to we have? Through petitions we can only get the commision to consider something so that is no efficient way. I think the EP election is the obvious target for popular demands on EU reform. Sure, the EP lacking powers is the problem, but the EP has some power to say no, to block things. Wisely used that can be translated to wider powers.

Say that we draft an EU Democracy Manifesto, spelling out a plan for greater democracy and then try to get candidates/parties to accept it (as many as possible). What would it contain?

Preferably actions should be tied to the increase of power. Take the case of wanting the Commission elected (for real) by the parliament. Lets say that the EP refuses to accept a Commission President unless the Council agrees to nominate the one the EP majority would elect, would it be up to them (either through a mock election or a demand of getting to choose between the candidate of the party groups or something). Then the manifesto would include somthing like:

"If elected, I will not vote to confirm a Commission President unless the European Parmliament through a fair and free election has choosen said Commission President."

So, what other powers has the EP, what other reforms are needed for democratising EU and how can the EP use it powers to enforce change?

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