Broken Base: Many fans were understandably upset that the Fully Absorbed Finale featured Frank having a very small role while Mulder and Scully solved all his problems for him. Others say that seeing him get a happy ending is such a relief that they could overlook it.
Raymond Dees, from season 1's "522666", is a Mad Bomber who derives sexual pleasure from the numerous deaths he causes. He initially blows up a crowded bar while watching the scene from afar. He later plants bombs in an office building, killing dozens more, and then participates in the rescue of the wounded simply so he can be hailed as a hero by the community. When Frank Black eventually discovers his true identity, Dees realizes that his game is up and arranges to be killed by the Feds so he can become notorious as a criminal instead, but not before taunting Frank with the possibility that he's rigged Frank's car to explode.
Yaponchik (aka Sergei Stepanovich, real name unknown), from season 1's "Maranatha", is a mass murderer who sees himself as an Antichrist figure with the mission to spread evil in the world. Taking inspiration from the Book of Revelation, he causes the Chernobyl disaster to kill many people and poison the land. A decade later in the United States, he kills a police officer and several people who tried to appease him, to re-establish his status as The Dreaded to the Russian community. He kills one of the two Russian officers who had been tracking him ever since Chernobyl by shooting him in public. He later goes on a killing spree in a bathhouse, before using religious fear to convince his nemesis Surova to help him escape so that he can continue his rampage elsewhere.
Avatar, from season 2's "The Mikado", is a Serial Killer who terrorized the streets of San Francisco in the 1980s, claiming nineteen victims before eluding the authorities. He eventually returns to broadcast his latest murders over the internet, kidnapping several women and presenting them on a website with a counter indicating the time until their deaths. He leads the cops to a remote trailer, planting deadly boobytraps after killing the previous occupant. When Frank Black finds Avatar's new lair, he tries to kill Black as well before disguising his latest victim as himself in the hopes that Black will shoot her by mistake. Avatar never speaks, but his huge body count and his sadistic games make him one of the show's most heinous villains.
The Chris Carter Effect: Also by Chris Carter, Millennium is a good example of this. The show got increasingly bizarre and difficult to follow as it went on, and the end of the third season (the last one filmed, and for good reason) provided no closure at all. Each season had a different show runner(s), each with a very different idea of what the show should be (Are Frank Black's flashes simply a visualization of his deductive skills or psychic visions? What is the Millennium group's agenda?) and no one from above willing to set boundaries. After the cancellation, the whole thing was put into the laps of The X-Files team. This resulted in a Fully Absorbed Finale for Millennium within The X-Files-verse that also failed to resolve anything.
Darkness-Induced Audience Apathy: This was one of the biggest reasons the show never caught on. The unrelentingly bleak tone along with the complete lack of levity made it hard to watch. While it earned the respect of the viewers able to handle it, most ended up alienated. Vince Gilligan, the man behind Breaking Bad and Better Call Saul, would cite the show as a writing lesson regarding this.
Vince Gilligan: "I would watch every episode, and afterward, I would just feel like I couldnt sleep at night, it was so dark. I guess that was instructive to me. That show told me, Be honest with your show, make it as dark as it needs to go, but youd better find a way to leaven it with humor, otherwise people are going to want to slit their wrists after they watch it.
Harsher in Hindsight: In episode 6, Frank and Catherine's young daughter Jordan starts asking about death. Catherine tells her that they will be with her forever. Catherine dies less than two years later.
The Woobie: Maddie Haskel in Season One's "The Wild and the Innocent." Her father abandons her, her abusive stepfather rapes her and is implied to be the father of her child, who he then SELLS to a rich couple so that he can buy himself a TV. Learning about this drives Maddie's mother to suicide. Maddie's abusive boyfriend is willing to take Maddie to find her baby, but in the process murders three people, which she is helpless to stop. She is willing to give the baby back to his adoptive parents once she gets to hold him, but is finally forced to kill her boyfriend to prevent him from killing her baby's adoptive parents and using the baby as a Human Shield against the police, and goes to jail for her part in everything. She describes Frank Black, who prevented the police from shooting her, as "the only man in my life that ever did something nice for me" and requests that her son never be told about her. All of this happens before she even turns 21.
Exactly, how did the Guardians determine who got to be a Chosen One? There seemed to be no distinguishing quality; one of them in fact turned out to be a racist bigot and was rejected. Another (Terra of the Teen Titans) was already dead, too. You'd think the Guardians would have known that.
Several of the Manhunter sleeper agents make absolutely no sense given their previous storylines. The worst, however, was the reveal that the entire town of Smallville had been replaced with robotic duplicates. Superman had no idea, despite having X-Ray vision.
Actually, this is incorrect. There was only one real Manhunter in Smallville, who took the place of the local doctor. This agent's plan was to plant a mind control chip in every single baby born in Smallville after Kal/Clark arrived in Smallville, so they would operate as sleeper agents. They would then subdue every single non-chipped Smallvillian, such as the Kents, and cause Superman to be unwilling to hurt them due to being innocent, especially Lana Lang. The fact still stands that in all his years, Superman never was able to see his family doctor was a robot or that every person in his generation and younger had chips in their heads is still ludicrous.
There is, however, an element of Fridge Brilliance. Even with his post-Crisis origin where his powers developed over time, it's likely a real doctor would have noticed something unusual about young Clark, especially since invulnerability was one of his first powers to begin developing.
Narm: Lots of it, but the crowning moment is probably when the New Guardians are first created; all the fancy logo-lettering for their new names is wonky enough, but each and every one of them is followed by a (tm), like DC isn't even pretending this mini-series isn't just one big toy ad anymore.
What an Idiot!: Harbinger, a character left over from Crisis on Infinite Earths, records the history of the universe in a device... which she leaves adrift in space for anyone to find! It was thanks to this that the Manhunters found out the secret identities of all the heroes.
Made worse by the fact that she barely gets reprimanded for it, and in fact joins the New Guardians.
Not to mention that the whole point of the Chosen, to become the first generation of people who would later give birth to generations to become the New Guardians, was made moot the moment they all became heroes: with a gay man, a walking tree, a giant floating face, a cyborg, a woman on fire being among the very small group of the Chosen, the possibility of them breeding was microscopic at best.