It's crucial in this regard to distinguish two issues: (a) to what degree do these institutions wield power unchecked by democratically-elected/legitimized institutions (President/Congress/Courts), and (b) those institutions commanding certain secret programs you (or I) disagree with (i. e. the stuff Snowden revealed).
Despite some regression in the last two years, there is still at least _some_ accountability, as the current whistleblower demonstrates. But, of course, the safety margin is shrinking. With enough turnover in some key positions, a future whistleblower may just find their legitimate complaint buried.