Complete Monster: The Astronomer was an old man with powers based on ritualistic magic, having willingly erased all the memories of his own life and starting a search for power which would lead him to the cult of the Egyptian Freemasons where he would become a high ranking member. Using his position to kidnap several women and use them as human sacrifices in depraved sexual rituals to empower himself, the Astronomer unwillingly gained the attention of heroic Aces that raided the Freemason temple. Leaving the cult leader to die in the raid to take the leadership himself, the Astronomer plans his revenge against the heroic Aces. He carries this out on the 40th anniversary of the Wild Card Day—where his servants injured and killed other Aces—in a murder spree while he personally dismembers Kid Dinosaur in front of his father and the general public. An Ace whose powers are literally based on his own depravity, the Astronomer was the first Big Bad of the series and one of its more monstrous.
Foe Yay: In the most disturbing way possible Blaise with Tachyon. He traps Tachyon's mind in a female body and rapes him/her.
Dr.Tachyon with his dashing cousin Zabb, goes from subtext to text, when Tachyon is trapped in a female body and starts a relationship with Zabb.
Harsher in Hindsight: In the opening of Inside Straight, it is stated that Egypt's new president, Kamal Farag Aziz was elected when "meddling Americans had forced a free election that swept out the secularists in power...". Inside Straight came out in 2008. Come Arab Spring (2011-2012) and the deposing of Hosni Mubarak, the Muslim Brotherhood won Egypt's first open election, making Mohamed Morsi president (until he was deposed in a military coup).
Ho Yay: Tachyon has it with almost the entire male cast. Since Takis does not have a taboo against homosexuality, and thus no Takisian is really homophobic, Tachyon's closeness with his friends, like his flamboyant behavior, can look like signs of homosexuality to humans. Especially since he is mainly living on Earth from the 1940's to the 1990's.
Idiot Ball: In Suicide Kings, a kid who has been shown to enjoy killing and has the power to blow up anything made of metal or stone is against a man with metal skin (Rustbelt) and proceeds to run away screaming rather than blow his head up.
Golden Boy wants to be the Woobie. However, the fact he's a supremely rich immortal Hollywood star with more girlfriends than God and SUPERPOWERS makes it difficult to sympathize with his 'woe is me' attitude.
The Sleeper has another case of these. His criminal activity makes it difficult to sympathize with his unique condition. Though it should be remembered that his criminal activity is done because he can't, with his sleep cycle, hold down a regular job; also it should be remembered that he was a 14 year old boy who in a few short (waking) weeks becomes a drug addict in order to keep from becoming a joker, and gets so addicted that he has to have one of his ace friends take pity and knock him out many times to stop his murderous rages.
Rustbelt. Every writer given his story refuses to give him a break.
Stuntman bounces between asshole and woobie. All of his dreams and aspirations never come true and, if they do, they're twisted like a joker. He wanted to play sports in high school, but he was even shy of 5'10, meaning scouters could hardly see him. Even his own father, a retired baseball player, said he didn't have the mentality of a sportsman, but an intellectual. He went to college and aspired to become an actor, but then his wild card turned, making him more desirable to Hollywood as... well, a stuntman, than an actual actor. He became a B-Movie washout and joined the cast of American Hero in hopes of restarting his now-dead career. Along the way, he lied and got Rustbelt, the nicest cast-member, discarded and branded a racist. And then he wins American Hero, but only because Curveball, the assumed victor, went to Egypt to become a real hero. And what happens? No one, not even his own parents cares because of the discards in Egypt were saving thousands of Jokers and defeating one of the world's most powerful aces. In Busted Flush, it's referenced that he becomes the "defender" of San Jose and has a bad stint on Dancing with the Stars. No wonder he joined SCARE.
Drummer Boy and John Hive get put through some seriously undeserved shit during their time with the Committee. Especially Drummer Boy given that he was tricked into being indirectly responsible for the deaths of several children.
Xavier Desmond, especially after he learns he has cancer.
Ensemble Dark Horse: Both Simon and the Sleeper's girlfriend have more fans than the author probably ever meant them to have. Especially since they both die.
Wangst: Alex seems to suffer from this as he seems more troubled by his superpowers than by his brother's death (and the deaths of his classmates).