Well, personally I didn't like this TAO arc either, since it's a major departure from TAO's modus operandi. He's never engaged any of WildStorm's heroes directly, or drawn attention to himself, but rather just worked in the shadows, played people against each other and kept a low profile. The thing is, in a fight he's nothing more than a human with extensive martial arts knowledge, what made him dangerous was it takes him less than an hour to hack the I.O. network from a library computer, and talking (he can reprogram people by having a conversation with them, or put them in a coma).
See, when Alan Moore revealed he was a badguy, when Fuji cornered him to arrest him, TAO instead said "let us reason together." A conversation later, Fuji was catatonic. He also set up his escape in a way he didn't encounter anyone else after Maxine, and only left a decoy to throw people off.
Later on, when Ed Brubaker decided to write a comic focused around the organization TAO had built up during the years away from the spotlight, Sleeper, he had TAO operate in a fashion that he'd draw no heat from people like The Authority (due to knowing that even Apollo or Midnighter alone would demolish his whole set-up). Instead, he operated Illuminati-style and just nudged and whispered around, and made use of super-powered goons only few of which ever even saw him or knew anything important. Anyway, I warmly recommend Sleeper, it's a great double agent thriller (the set-up is that Lynch sent his protege Holden Carver to "go rogue" without telling anyone except the two of them, so TAO's crew would recruit him. Well, happens to be that TAO manipulates Grifter into shooting Lynch in the head and leaving him in a coma, so Holden is now really rogue to everyone's knowledge and is trapped in a supervillain organization).
EDIT: Oh yea, it also bears mention that Alan Moore's story's last twist was that Majestic hadn't killed TAO, but a shapeshifter decoy named Mister White he had "reasoned with" earlier. The only one who knew TAO was alive was Savant, who he had sent a letter and knew was too much in his thrall to tell Majestic about him being alive. Since he knew that being an old breed superhero with unimaginable power and intellect, Majestic WOULD find him and WOULD kill him without him even being able to react for what he did to Savant, Fuji and Maxine.