Some one-sided Ho Yay for both Koutarou and Yoshida. Both almost seem in love with one of the Twins (Kazuya for Koutarou and Tatsuya for Yoshida). Tatsuya even jokes that Koutarou is like Kazuya's wife and tells Yoshida he's "just not into that kind of thing."
Koutarou is the catcher, and "wife" is a common slang term for the catcher half of a pitching battery. Koutarou even uses the term sometimes. "I'm a widow!"
In an early Day in the Limelight episode Koutarou goes into a slump because he thinks a girl he likes doesn't like him. He proceeds to tread dangerously close to I Want My Beloved to Be Happy regarding Kazuya and, when he learns that she does in fact like him as well, he glomps onto Kazuya and never mentions her again.
Koutarou basically admits that he was only playing baseball to be with Kazuya, and after Kazuya dies, he threatens to quit the team, saying that running up to Kazuya's smile after a game was "the only thing [he] lived for". Entire essays could be written on the subject of Koutarou's feelings towards Kazuya.
"Don't leave me alone, alright? For a second time."
What an Idiot!: Coach Nishio and the school headmaster approving Kashiwaba to run roughshod with coaching the school baseball team with his ruthless and abusive style despite the former not having seen him in years and the latter allowing him to coach without being questioned for his actions. This not so smart choice nearly led to the school baseball team's utter collapse.
Jerkass Woobie: Calvin, he did kidnap a kid but he meant to send her back to her family eventually, was trying to save his brothers life, is never a Jerkass (despite the name of the trope), is willing to help the main characters eventually and has to go through losing just about everything by the end of the finale.
Moral Event Horizon: In the Season 2 episode "Eye to Eye," Guillermo goes into a church to confess his sins. When the priest goes to the police station with the intention of revealing what has happened, Guillermo follows him in and slits his throat with the Tree of Life knife. This after in the previous episode, Avram told him that deviating from his mission would reduce him to merely a "godless murderer."
Clea, given her strong presence in season one and how she doesnt even get a mention in season 2 despite limited closure.
Some of the other righteous 38 (an I Just Want to Be Normal woman who uses the numbers to be an architect, a baker who used the numbers to compose a beautiful piece of music and a man who became an army medic and saved lives with that knowledge) feel like they could have have been great supporting characters instead of Victims for Guillermo and a faulty AsterCorp drug respectively after just a few minutes of screen time.