The main character, Zee's origins are explained within the opening paragraph of the main page. He is the de facto hero of the series.
Actual Pacifist: Would only use force to save human life, and only when it was the only option available. He refused to use guns to any degree and though it's implied he was strong enough to kill people, he never did much more than knock them out, if that.
A.I. Is a Crapshoot: Was programmed to be heartless, emotionless, and a hitman. He ends up becoming a sweet, gentle, loving soul who's a rare male version of Friend to All Living Things (although this is sort of the best possible scenario you can have when your A.I. goes awry).
Badass Pacifist: Despite being designed and programmed to be an assassin-bot, he refuses to carry weapons, or ever attack or harm a human being. He faces down an impressive number of foes, including those more than willing to use deadly force on him, his Action Girl companion, or bystanders, without ever once violating this (excluding the rare occasions where he is under the robot equivalent of Mind Control). This is the result of his character development in Batman Beyond, where he started out willing to use force against his enemies.
Children Are Innocent: Though adult in appearance, he hasn't lived long enough to get jokes, slang, or innuendo, and seems to take people at their word most of the time. He's also a terrible judge of character due to believing the best of people. When he's shape-shifted into child form, even the other kids find him ultra-naive.
Dead Person Impersonation: Was programmed to be this way, but his A.I. eventually evolved into an actual personality and he decided he no longer wanted to continue killing and imitating his victims.
Horrible Judge of Character: Trusts everyone inherently and believes everyone is good deep down. He also can't seem to gauge when people are lying to him, no matter how obvious it is.
I Am Not a Gun: Or in his words, he doesn't wish to destroy anymore. In addition, his statement that "I decide who I want to be" could count as this.
Innocent Innuendo: Anything that he says that sounds even remotely suggestive is this. He really, really doesn't get it. Special mention goes to kissing a complete stranger and not knowing why Ro was upset.
Not Helping Your Case: He's accused of being re-programmed by a terrorist, and no matter what he does the FBI always make it out to be a crime. During most of the series, he was pursuing his creator so he can convince them that he's good, but his actions are taken as an assassination attempt when he accidentally set off the cryogenic chamber, almost killing him. The poor guy just can't win.
Love Redeems: The creator has admitted it comes across as ambiguously psuedo-romantic, but it was intended as platonic. It's more his love for the child of the man he's impersonating than the wife that makes him begin to change anyway.
Screw the Money, I Have Rules!: Literally has no reason whatsoever to be as moral and kind as he is other than free will. His morality and heroism are self-enforced standards and as such he cannot be bought off, bribed or threatened.
Wide-Eyed Idealist: Naive and kind, always taking people at their word, a terrible of judge of character who thinks the best of everyone and generally easily manipulated. It's due to being so young and having no knowledge of the world beforehand, and to be fair, his friends do try to help him get better about this.
Depending on the Writer: Sometimes he's willing to let a known terrorist (Mad Stan from Batman Beyond) run around without diverting his considerable resources to stopping him and saving lives simply because it's not his problem. Other times he berates West for opening fire in a crowded place, seems genuinely concerned for those around him and goes out of his way to keep people safe. He also varies from being all business to somewhat friendly towards Lee.
Not Helping Your Case: When he tries to convince his superiors in season 2 he hasn't gone insane on this mission, the fact one of his own Agents left the NSA over his behavior is pointed out. He counters he hasn't had a bad call on his record other than Gotham, which is not a good incident to bring up since he nearly got part of the city blown up during that incident. Agent West facepalms audibly in the background.
Parents as People: He's an absentee parent, but only because his job's pay is directly in proportion to how many assignments he takes. He and his son have issues about this and resolve it as best they can. His Sanity Slippage actually regresses when he's allowed some normal family time.
Action Girl: In contrast to her wimpy partner, Lee was able to hold off a mercenary with her hands tied together.
All Asians Know Martial Arts: Averted. Her fighting style is identical to every other Agent we see in the series. Agent Rush actually has the most kung fu esque moves out of all the Agents, and he's black.
The Commissioner Gordon: Developed into this after Zeta saved her life at great personal risk to himself. Unfortunately, she's not in as much power as most examples, so actually helping him out is hard.
Not Helping Your Case: Goes back and forth: initially she gets this when trying to explain Zeta isn't evil, but she's Genre Savvy enough to try that exactly once and then turn to the much more provable and equally true objection to her superiors that Bennett is becoming unstable. When she feels it isn't taken seriously, she quits, an act extreme enough to prompt investigation into Bennett's behavior. But she can't get Zeta's case heard afterwards when she's viewed as a Mood-Swinger who turned on her boss, and any response she has damages her case.