Lucci's flaw was that, as the perfect governmental assassin, he always followed orders, not caring for anything. He wouldn't get angry nor glad, happy nor sad... Lacking personality, the readers couldn't identify with him in any point, so he seemed the most powerfull, yet the most boring, of all CP9 characters...
Of course, that's how I saw him. Lucci's fans are free to show me how he can be interesting.