Broken Base: The difference in format between the first and second half the series. The first half of the series is largely an episodic Monster of the Week formula, with character development and the main plot taking a backseat. While some fans feel this is a boring start that drags down the rest of the series, others feel its needed to establish the world and its themes.
"Loaded Guns", which ended the show's Monster of the Week format and started its main story arc.
"Raindrops" is when the show's Monster of the Week's storyline became more emotionally and dramatically investing
Jerkass Woobie: Amon. His mother was a Seed who awakened into a Witch. This changed her drastically and ruined their relationship, making him fearful of the chance he might awaken one day. It's not helped when his former partner became a Witch and went rogue, forcing him to kill her.
At the end of the series, the STNJ goes back to hunting. With the second half of the series dedicated to showing sympathy for the Witches and The Reveal of Zaizen's activities, you'd think the nature of hunts would've changed, especially as characters can no longer rely on orbo. This is left unexplained in favor of Status Quo Is God.
Robin. With the second half the series, after spending half the series hunting witches, she finds herself being hunted. To start, she has to watch her roommate get used as a hostage and put into a coma, the STNJ raided, and Amon apparently killed to save her. Then she has to deal with powerful witch hunters being sent after her, including by her mentor.
Michael. He reveals early on that he was a hacker forced to join the STNJ after hacking into their system. He's not even allowed to leave the building, since he knows too much.