If this detailed but thinly sourced Der Spiegel article is to be believed, all is not well at the Vatican. A closer reading, to me at least, reveals more about the assumptions and expectations of a modern secular political writer than it does about any particular set of scandals in the Curia. It's also quite striking how similar this is to the kinds of stories that come out of the Pentagon when the Secretary of Defense tries to get anything major done. Massive, insular, wealthy, and powerful organizations run by humans seem to have commonalities.
The unfortunate truth, and to me it seems that the author can't quite get his head around the fact, is that the Pope is not a bureaucrat, and he is not an elected official in the popular sense. He's the head of an independent state with an organizational memory that goes back to the time of the emperors of Rome. The papacy has survived far, far worse than whatever it might actually be going through right now. It will continue.