One thing I want to know: What keeps a super secret agency, that is not accountable to anyone but itself, from taking over the Federation (covertly or overtly) in order to protect it?
With The collaboration between StarFleet Command and Section 31 we can presume they are accountable to StarFleet Command and the Admiralty. Section 31 is outside StarFleet Intelligence and Starfleet security. I believe Section 31 is only invested in protecting Earth and humanity above all else. They are sanctioned in the first Earth starfleet charter. Taking over the entire Fed would be a challenge with the hundreds of worlds and not every starfleet vessel is run only by humans. They could theoretically take over Earth and by extenstion the Fed like that one Admiral did in DS9 Paradise Lost. But expect a resitance nd secession from the Fed if that happened.