What if we've been strung along for a while now and that neither Waltz nor Scott are the "main villain". Here's my very loose theory.
An agent of SPECTRE, possibly high up in the ranks, is entered into British politics to bring down MI6 from the inside. His name - or cover - is Gareth Mallory and he goes deep under cover, rising among the ranks of the Intelligence and Security Committee and, eventually rising to Chairman - giving him a say in the running of MI6.
SPECTRE knows that Dench's M is extremely loyal, and would not bow to bribery, corruption or blackmail and they need to get rid of her some way or the other. At the start of Skyfall, we see Mallory pressuring M to retire.
During the events at Skyfall Lodge, M is K.I.A and Mallory takes the opportunity to put himself forward as head of MI6 - given his "military background" - either real or invented and planted by SPECTRE using their various moles and contacts in the various military sections.
Mallory is now M, a member of SPECTRE and head of the British Secret Service.
Bond, being Bond, happens upon the information that a member of this far reaching terrorist organisation has planted a member in the ranks of MI6 - he does not know who and knows that he can trust noone.
He carries on the mission assigned to him by M, but secretly investigates his concerns on the side - building up his suspicions and evidence so that he can act without SPECTRE or the Mole catching on to his investigation - who can he trust, who can help him in his mission that wouldn't compromise his search?
