If I understand Skyfall correctly, James Bond's primary mission is to protect M from being killed by Silva -- despite this, near the end of the movie, M dies from a wound inflicted by Silva's men.
Earlier in the movie, Bond had been tasked with preventing Silva's distribution of the names of MI6's undercover agents -- but Silva was able to begin distributing the names, resulting in the deaths of multiple undercover agents and a public inquiry into MI6.
Also, Silva successfully detonated bombs in MI6 headquarters and in the London Underground.
With all this in mind, did James Bond fail his mission in "Skyfall"? Bond managed to save his own life and to kill Silva, but virtually all of Silva's plan seemed to succeed.