That said, I don't like it too. No real transparency or accountability is always bad. And I'm not saying the EU is perfect - far from it! - I'm just saying that where it's not perfect it is because it is a big compromise between people wanting a federation and people wanting to keep their power and an economic union.
How is that undemocratic?
How is that democratic?
The member states themselves (which sorry, democratically speaking means their citizens) want to keep the council more powerful than the parliament. Fixing the power disparity has always been hard, since the member state don't really want to give away their power to the EU.
Anyway, a "no" vote from the EP means a great deal, your information seems outdated to me. The EC can approve a law proposed by the commission alone only in a restricted subset of topics. Everything else is dealt with with the parliament and the council being on equal footing and acting as a bicameral democracy with equal chambers would when approving a law.
The alternative of the current system is to reduce the power the member states hold in the EU creating a real federation or US of Europe. Which for sure will not happen in the short term, and if the EU does not react correctly (and strongly) to this vote, probably never will.
How is that democratic?
As for the EP. 1. It is composed of amateur politicians. 2. They are effectively powerless. 3. They can easily be bought.
The EU being anti-democratic sounds like a case of "citation needed" for me. What major problems remain after the 2009 changes?