I am a fan of Section 31. I like the shades of gray aspect a lot. I don't think Section 31 has always been depicted as the most competent organization though, and Into Darkness at least keeps that part going.
Well, if you just stick to DS9, Section 31 is pretty competent. Their only failure happens when Bashir and O'Brien capture Sloan and enter his mind to get the cure to the Changeling virus.