[spoilers] Lucas. Just Lucas.

[HellsBells]

I agree that there was not enough time given to the story that Lucas is John, we had two series to develop Lucas's character but only one to destroy it.
I think it may have worked if John wasn't so evil and Lucas wasn't so good. How can you go from being a 'hash-head' (mentioned in the 9.7 commentary) capable of the premeditated slaughter of innocent people to an excellent top MI5 recruit?
Disappointingly there was no mention how Lucas survived the torture in the Russian prison without revealing his true identity.