The commission basically represents the governments of the individual member countries. Because it has the most power by far of all the european institutions, this means that the governments in turn can exercise power at the EU level in a fairly unimpeded fashion.

If the legislative power were transferred away from the commission to the parliament (where it should be, if EU governance were to follow the standard approach for separation of powers), the individual member states would lose a lot of control. Control they aren't at all interested in relinquishing, as you may imagine.

And that's before even considering making the executive branch (the commission) directly elected.

In principle yes, but in practice that's not always the case. Once chosen, a member state can't remove a commissioner, even if they're willing to. Simply there's no way. Now they have to wait until 2014. Imagine that some political party has (actually) appointed a commissioner because they won the national elections, not much democratic but it's something. Next election they lose, and the new government can't change the commissioner, where's democracy now? If only the commissioners would be elected at the European Elections, the whole Commission idea would make some sense.

> Next election they lose, and the new government can't change the commissioner, where's democracy now?

This is standard practice in all civil service jobs, as well as the judicial branch.

You can't just remove a judge, or a bureaucrat because his party is out of office. Doing so, ensures that there is continuity and stability between governments.

You're absolutely right and things should work that way. But these are in fact political appointments yet their point is to give the member states a sense of entitlement. Once the voters have lost their confidence in the political party to which the commissioners belong, there's no reason for them to be there, as they really haven't been elected by the people. Moreover, they are unlikely to play second fiddle any longer, the temptation to stick to their own narrow agendas is just too strong. Keep in mind that these people are professional politicians, not technicians.

It's actually about perception — the Commission is selected by the governments in a diplomatic process. Of course the reality is way more complicated, but in this particular case the perception matters a lot. This is quite unfortunate, and changing this perceptions is, in my opinion, one of the foremost challenges to euroenthusiasts like me.