It allows the president to bypass Checks and Balances, by giving him a separate organization that is entirely devoid of the checks and balances system. Our Government was made to counter-balance itself, so nobody gets too powerful, but presidents have been using the CIA to make the Executive office more and more important ever since it's establishment.
Sounds like it fits the bill, but could you give me a little more info, maybe some specifics? I don't know much about it.

And what should we do about the situation, in your opinion? The CIA has to be better than having no intelligence agency, right? Even if their wrong or crazy the majority of the time, wouldn't it be better than having our heads in the sand?