Base-Breaking Character: Yukari. Some fans will take any chance to bash her for her reckless and authoritarian behavior and general hypocrisy, as well as the shitty way she treats everyone else. Granted, it's not exactly undeserved, but some take it more personal than others. The author himself acknowledged that he didn't anticipate such a strong reaction.
Rin Satsuki. Underneath a mostly cheerful and heavily unstable exterior lies a past full of pain, abandonment, abuse, and, more recently, everyone on the list of the "big names" of Gensokyo trying to kill her. Her only "friend" is her youkai companion who in return really dislikes her. No wonder that she snaps after the Battle in the Center of the Mind. Plus, Kirin society very literally considers her mere existence as an abomination, simply on account of being an unplanned child.
Kotohime qualifies, because she has the disadvantage of being a mere human trying to do her job and has to deal on a daily base with monsters, lack of recognition and problems in general. And she still doesn't give up.
Jerkass Woobie: Cirno may have been a bully and a prankster at the beginning of the story (as well as plenty of years before that), but damn can you not help but feel bad for her after getting beaten up so much, mainly by Marisa and then Yukari, and all that happened to poor Rumia which starts up the plot. The rest of her gang may count too.
Les Yay: Being a Touhou Project fanfiction, it's almost required to at least have hints of this, such as Marisa's frequent sex jokes, or Wriggle being mistaken for Mystia's lover, or Rumia admiring Kaguya and Mokou's bodies, or Yuuka's... affection towards Wriggle, or the Shadow Youkai threatening to rape Reisen as part of a To the Pain speech.
And how can we forget this phrase Yukari said to Yuyuko:
Yukari: [as Yuyuko carries her in her arms after a fight]: You...do realize...this doesn't mean...we're going steady.
It's also discussed In-Universe. For example, there are some... rumors... about the relationship between Marisa and Alice.
"If anything, [Reimu] hoped that those two would move beyond subtext and make official such a relationship. Threatening to tell Alice whenever Marisa started to get out of line would at least make it easier to control her."
And how could we possibly forget Rin and Rumia's Innocent Innuendo-laden conversations?
Nue also admits that she went after Rin not for the bounty, but just to protect Byakuren. Oh, and that she loves her, too.
Misaimed Fandom: Yuuka in-universe is a monster, but some readers gladly overlook some of her mostvillainousacts, because, among the main villains, she's still the one who gets the most (if not the only one) Pet the Dog moments. Of course, they may have some other reasons.
Not Badass Enough for Fans: Rin suffers from this. She has received a few criticisms for being a weak character, but it must be considered that she resisted to the psychological attacks of the Shadow Youkai (to which, if she had broken down, Gensokyo would probably be no more) and always tries to find a solution.
Shocking Moments: From the spin-off Touhous IN SPACE, Yuugi being launched out of a cannon, into the cold vacuum of space, right through a magma barrier and punching Yukari's flagship in half, surviving the whole ordeal. All while not spilling a single drop of sake from her bowl.
