Let me first start of by saying: I generally don't read shounen. Code:Breaker is probably one of the few shounens I read.
The premise isn't particularly new - evil vs evil, people with superpowers and abilities, a corrupt government. What is the breaking point for any manga for me is it's characters. And with a shounen, you're bound to get many.
The female lead, Sakura, disappointed me at first. She was branded as a 'strong female lead' but I saw nothing of such, apart from literally being strong. She was annoying with her whole 'don't kill!' and pretty much stupid for jumping in the dangerous situations.
BUT she does grow on you. She's such a contrast between the Code:Breakers and their whole quest for killing and revenge that it's refreshing. She's got strong morals and voices them. Countless times. I consider that strong, for not conforming. As the manga progresses, I become more sympathetic to her plight and we eventually do understand her aversion to death and killing.
The male lead, Rei is the typical kick-ass, silent but deadly killer. I don't have any complaints about him. Sure, sterotypical but I like his character, killing tendencies aside. He too, slowly grows with the influence of Sakura.
The rest of the characters have diversity and it's interesting to see their compelling needs clash between their friendships.
So far, I've found it enjoyable enough.