A lot of people seem to be saying in this thread that because Section 31 is not 'constrained by morals or accountability' that it is inherently more effective. It's far more likely that it ended up being, for those of you who've played Mass Effect, Cerberus. An organization led by a man who substitutes his own political feelings for the 'Best interest' of the Federation. Yeah, it's very effective at achieving its goals, but those goals are all about the organization's best interests, not the best interests of the constituents they supposedly exist to protect.
That is not to say that the Federation was not really negligent in its intelligence gathering leading up to the Borg and Dominion threats. It was naive and complacent, but that doesn't justify circumventing a perfectly stable, open and merit-based command structure through a violent, surreptitious coup because you disagree with its decisions.
Do you honestly believe that Section 31 has actually contributed to the safety of the Federation? Or is it far more likely they've simply grabbed power for themselves under the justification of the safety of the Federation?