These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Ensemble Darkhorse: Judging by Watase's notes in the backs of some volumes, Kannagi does very well in character popularity polls.
Foe Yay: Hinohara and Kadowaki. The more overt hints don't come until after The Reveal that the two used to be friends. Sort of lampshaded when Miyabi suspects that Kadowaki actually likes Hinohara, then immediately adds that she doesn't mean it in a "weird" way.
Not much yet, but Hinohara seems to like Kannagi's transvestite version way too much. Also played with during the Kugura arc, wherein Kugura falls in love with a cross-dressing Hinohara, much to the latter's chagrin. The Bishie Sparkle that Kugura views Hinohara with after the Unsettling Gender-Reveal don't help matters much.
Rami's declaration of "Mikusa-sama's the only one for me!" isn't so Les Yay to the cast who are in the dark about Mikusa's true gender, but it's another thing for the audience who found out before the characters. Even Kotoha, the only other member of the group to know Mikusa's secret at the time, admits to being impressed by the strength of Rami's love.
Hiruha, originally one of Kagura's Zokushou, later chooses to join up with Hinohara's team. He says that it's because Hinohara looked cool when fighting Kagura, blushing as he says it. He later leaps on the opportunity to ask Hinohara to wash his back during the Hot Springs Episode.
Nightmare Fuel: Chapter 23, "Behind the Curtain", makes chilling use of the Gory Discretion Shot. The double-spread in chapter 46 that introduces Orochi ain't pretty, either - not to mention what Orochi can actually do to people, as we see with Eto later on.
The Scrappy: People aren't fond of Kadowaki. There are characters who are jerks, but popularbecause they're fun to watch, and then there are jerks who people hate just as much as they would hate if they were to encounter them in real life. Kadowaki is the latter. He's a bona fide rich kid Jerkass whose only justification for his cruelty to Hinohara is the fact that he has a neglectful father and that Hinohara is better than him at sports. Naturally, when he comes to the other world to hinder Hinohara's efforts to save it, his hatedom only increases. Once in the other world, he reveals himself to be a full-blown sociopath: he treats everyone like crap and sets out to kill powerful Shous just to gain power, and ruthlessly kills anybody who gets in the way of an already murderous goal. The biggest problem with this series is that this fucker isn't dead yet.
They Wasted a Perfectly Good Plot : The setup seems interesting with Arata pretending to be a maiden, getting framed, they switch....and it turns into a fairly normal Trapped in Another World type thing. It's well executed an all, but it seems like there was a bunch of awesome in the setup that just didn't get used.
Wangst: Depending on your sensibilities, the backstories of some of the Shou may or may not feel like this. Hinohara is typically considered guilty of this more often than the others.