Back in 2007, the former NotW Royal correspondent Clive Goodman and private detective Glenn Mulcaire were jailed for accessing the private voicemails of eight people; it is now coming to light that the Met had lists of, in the words of a CPS file seen by the Guardian, "a vast number of unique voicemail numbers belonging to high-profile individuals (politicians, celebrities) [who] have been identified as being accessed without authority". Questions are being asked of the police why they did not expand their enquiry to include these people, which could have brought other NotW journalists into the investigation. The NYT article says phone hacking was widely practiced at the paper and that the then editor Andy Coulson - now David Cameron's Director of Communications - was aware of it (Coulson denies any knowledge).
The NYT also implies that the Met's "symbiotic relationship with News of the World" affected their willingness to fully investigate the case, something Yates refuted this morning. The Guardian - one of the few papers to fully report the story from the outset - has a comprehensive list of issues any independent inquiry into the Met's handling of the case will want to look at.