anyone (including of course Council and EP) can propose policies : but the Commission has the monopoly of legislative initiative. In other words, only the Commission can make proposals for directives and regulations (the main EU legislative acts, which are the practical embodiment of policies). Of course, the Commission will draft proposals which stand a chance of being adopted (even if only in some amended form) by the legislative power (i.e. Council and EP) ...
There are many decisions which are taken by unanimity in Council. Not only in foreign affairs and security matters (where the EU has certain competencies, in any case). Check e.g. fiscal policy, some areas of justice and home affairs, social affairs etc check
http://www.consilium.europa.eu/en/council-eu/voting-system/unanimity/ for the areas where unanimity in Council is necessary
totally irrelevant. The Junker Commission (like any national executive) was approved by both arms of the legislative (Council and Parliament). This is exactly how most of our constitutional systems work, and nowhere is it written in our constitutions that Ministers are directly elected by the electorate.
the EP is far from powerless. It has equal say with the Council on most matters : the main exception being foreign and security policy . It gets however to approve external agreements, if they modify legislative acts, if they have important budgetary implications, or if they set up specific institutional structures. In many ways, the EP has more power than National Parliaments, since in it there is no pre-constituted majority which will rubber-stamp what the Executive (Government) proposes. It is more similar to the US House of Representatives , in this respect
In a nutshell : it is true that the EU constitutional structure is inevitably, in many ways, "one step more removed" from the electorate (as many federal systems are). All of its organs, however, are (either directly or indirectly) responsible towards the electorate
In particular, the Commission is directly responsible towards the EP and can be removed by it (as happened years ago to the Santer Commission)
The main difference with our national constitutional systems is that unanimity in Council is required for some decisions (and this, of course, means that in some areas anyone of the 28 States has, in practice, veto power - a recipe for inefficiency and blackmail)
also, the fact that the executive (Commission) has the monopoly of legislative initiative : however, this is largely irrelevant. In most of our systems, acts are anyway adopted on the basis of a proposal made by the executive, even if such a monopoly of initiative does not exist
In my view, the main "democratic deficit" depends from the fact that a European "public opinion" does not yet exist, and that information on EU matters is still very summary (as, e.g. your post demonstrates)
best