Federal agents say the use of Tor and Bitcoin were major obstacles for them and that investigating the site was “uncharted territory” that involved a reversal of their usual investigative methods. Instead of starting with probable cause against a specific suspect who is already identified and then obtaining a search warrant to collect more evidence, the investigation of Silk Road involved collecting evidence from the site first and then trying to identify individuals.
Sure it is "uncharted territory" in terms of the technology for maintaining anonymous identities, but shouldn't most investigations start with evidence of the crime and an empirical investigation into who could have committed it, rather than starting with suspects and trying to link them with the crime? Maybe I am naive, but sounds like dodgy criminal investigation methodology to me...