Ensemble Darkhorse: Flay, some people play this game just to use him (and it may have influenced Gust's decision to keep him in the sequel, as well as canonize his ending).
Fan-Preferred Couple: the only ending with a confirmed romantic implication (not counting Vayne-as-queen in Muppy's ending) was with Nikki. And yet there's a lot of fan support for Vayne/Jess. First Girl Wins?
Fridge Brilliance: Of course students are allowed to heavily customize their uniforms. It's an alchemy school. Modifying things to make them more effective is important enough to be a game mechanic.
Fridge Logic: Flay is a Senior, and that apparently allows the True Companions to venture the Mana Ruins - Interior Heights. So, why not include the God's Scar and Clocktower into the list?
So Theofratus makes a Mana capable of granting any wishes to atone for his mistake for shortening Jess's lifespan, right? But, WHY THE HELL DID HE USE IT TO KILLS HIMSELF?! Does he ever think that he can use it to fix that mistake? To makes Jess healthy again? And he is supposed to be the most brilliant alchemist ever...
Arguably applies to Vayne as well. Why didn't he think of using his reality-altering power to cure Jess before giving it up?
He does if you follow her route. In Jess's ending he offers to make that the last wish he ever performs but Jess turns him down on that offer.
Regardless of the fact that Vayne can potentially end up with anyone in the True Companions, members of said group seem to have a fondness of citing his interests towards another character (Jess, in her second-to-last and final Character Quests, for example). Or...lack thereof, in Pamela's case. "This is Vayne we're talking about; that's impossible!~"
Like You Would Really Do It: Like anyone would die. Really. Really, there's no sarcasm in this statement. The bad ending doesn't count.
"A Quiet Giddiness", the final school theme that plays during the later, Mood Whiplash chapters of the game. A technically excellent song, but the sheer trepidation of it and the fact that it's played everywhere you go in school from then on, in contrast to the first, almost absurdly upbeat school theme, makes it quite hard to bear during those moments when everything's falling apart.
Vayne's special attacks all involve shadows, lots and lots of sharp blades, creepy red eyes, and surprisingly violent battle quotes. So it makes sense that the final boss is a horrible mass of red eyes that cry black gunk. Oh, and his true power is pretty scary too.
When Isolde kills one of your friends to force Vayne's powers to surface, you have to think: what if Vayne wasn't able to bring him/her back, and Isolde took the leap from slightly unbalanced teacher to murderer? Even worse than that, she didn't even flinch when she killed them. If Vayne couldn't wish him/her back to life, what was to stop Isolde from murdering all of them right then and there to keep said murder a secret?
Player Punch: Before the second boss battle with her, Isolde crosses the Moral Event Horizon and kills one of your party members to force Vayne to use his powers to revive them, proving he's a Mana. Which party member gets killed depends on which one's character quests you did, which probably means that you have an attachment to that character. Of course, since Vayne's the Mana of Wishes, they get resurrected quickly, which can lend itself to Narm, but damn if that didn't piss the party off. And the player too, maybe.
That One Boss: The second round against the blue-haired teacher. She basically spam activates a thunder attack that puts alot of cards on the battle sequence, clogging up your moves, and does a two round mass-kill attack, unless you can block it, or use defensive supports. You need a ton of mass revive items, and even then, you'd probably still die.
Goddamned Boss: ZweisMunde (literally "two worlds") is actually a fun boss, but really loves to use Interface Screw attacks. One of them turns all your healing echo (and other multi-card techs) into its own multi-card attacks. Another one swaps out your entire team.
The Scrappy: Tony. The guy is your typical stuck up asshole who has a grudge against the protagonists. His only redeeming quality is that he's so pathetic it's funny and that he's a threat in boss fights.