In the Anime, after Evangelion Unit 01 eats Zuruel's S2 Engine in it's beserk mode, Gendo is seen in a meeting with the member of SEELE or whoever the pseudo-illuminati style organization is running NERV from the shadows. One of the directors of the organization states Evangelion Unit 01 has become self aware, almost becoming god-like, and that they have no use for a god in their master plan.
Now I fail to see how a sentient EVA Unit can prove to be such a hindering factor in SEELE's ultimate plan. How could one EVA Unit pose such a threat to the plan that the Unit had to be grounded until further notice? and what type of hindrance were the SEELE directors talking about?