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.
The Obsidian Lord. This guy arranges the entire Hime battle to make sure the Hime lose their loved ones so that he gains power from the battle, in during the battle in question in this series he plans destroy and re-create the world due his dislike for how Japan has become.
Die for Our Ship: Shizuru x Natsuki fans bash Nao. Nao x Natsuki fans bash Shizuru. Mai x anyone else fans (Mai x Mikoto fans in particular) bash Yuuichi. In the manga, fans of Shizuru x Natsuki bash Yuuichi because in that version, Natsuki is attracted to him instead.
Nao is quite popular, despite luring in and robbing men via Enjo Kosai as a means of getting revenge, and kidnapping Takumi, indirectly leading to his death, and later attacking Natsuki a few times in revenge for her eye being put out.
Shizuru's fans tend to overlook her actions, including killing Yukino's child, leading to Haruka's death, killing Nao's child, leading to her mother's death, and destroying the First District Headquarters. What exactly happened with Natsuki in the incident Yukino witnessed is less clear, though.
Interestingly enough, some of Shizuru's haters actually forget the First District's real goals when calling her destruction of its headquarters her Moral Event Horizon. It's arguable how much the Mooks knew about the plans or how necessary killing them was, but trying to pass off the leaders as victims clearly falls into this trope.
Ending Aversion / Broken Base: Opinions vary on the ending. Is it the happy ending that the characters deserve after everything they went through, or is it a betrayal of the series' tone?
Ensemble Darkhorse: Of the side characters, Shizuru is the most popular, despite some of her transgressions in the last few episodes of the anime series.
Fan Preferred Couple: Shizuru and Natsuki, also known as ShizNat, overwhelmingly so. The Mai-Hime section of fanfiction.net has more Shizuru/Natsuki fanfics than there are all other stories combined.
"Funny Aneurysm" Moment: Reito jokes about it being "dangerous" to leave Shizuru to tend to a sick Natsuki by herself in the audio dramas. Shizuru later kisses Natsuki while she's asleep (and might have gone further slightly before that), and also angsts quite a bit about her feelings being improper, which at least one other person (Haruka) also agrees with. One could see it as a case of Reito being more on the mark than he might have realized, and/or that the joke helps reinforce Shizuru's belief that it's wrong for her to love Natsuki.
In the prototype trailer, Mikoto performs a Dynamic Entry on Shiho, kicking her away from Mai as they're engaged in a tussle. In the actual show, when Shiho attacks Mai with her Child, Mikoto intervenes to save Mai, destroying Shiho's Child and thus killing Yuuichi, the boy Shiho and Mai love, in the process.
Het is Ew: Most of the heterosexual pairings besides (or especially) Akira/Takumi (and even then, Akira is pretending to be a boy for much of the series) get bashed.
Hilarious in Hindsight: In early episode, some of Mai's yaoi fangirl friends imagine a romance between them because they find both of them cute (not knowing that Akira is a girl), before Mai tells them to keep her brother out of their Crack Pairings. And later in the series, Akira and Takumi do seem to be romantically involved.
Jerkass Woobie: Nao. She's bitter, hostile toward most people, goes to great lengths to avenge her losing an eye and robs perverts for fun because her father was killed and her mother went into a coma during a robbery.
Launcher of a Thousand Ships: Shizuru is the show's "crown princess of yuri", who probably has been paired with any named female character close to her age, though most fans prefer to ship her with Natsuki.
Les Yay: Mikoto's behavior toward Mai, naturally giving way to plenty of Ship Tease moments between the two. In reality, Mai feels more comfortable being Mikoto's Cool Big Sis, though it's rather blatantly implied that Mikoto wants more than that.
Mikoto: (* grabs Shiho's hair* ) Those are my melons. (* tosses her aside, glomps Mai herself, and starts nuzzling Mai's chest* }
Not only does Shizuru have her very close friendship with and romantic feelings for Natuski, but in one of the sound dramas, "Lingerie Rhapsody," she's very pleased to check Mai's bra size (including even putting the bra on her), and notes that she's quite attractive. Natsuki implies that Mai is inwardly enjoying it all.
Mary Sue: Haruka Suzushiro, who was a somewhat complex Badass Normal in the anime, was turned into probably one of the most powerful Himes in the manga, and it shows (although she and Yukino lose to Natsuki and Mai). There's also some favoritism skewed in her favor over Shizuru; just go read the chapter where she's having a hallucination inside Yukariko's Child.
Moe: Mikoto, she's extremely cute and her childish behavior makes her even cuter, notable examples include a scene where she grabs onto Mai and clings to her for the better part of a day, and Mai isn't even particularly bothered by it, having apparently gotten used to her acting this way by that point in the series.
Narm: John Smith's name is quite amusing because it seems to be an obvious pseudonym and sounds strange when the characters try to say it in the Japanese version. It gets even funnier if you're familiar with Haruhi Suzumiya.
Paranoia Fuel: So many characters are not what they appear to be, in a negative sense, whether their positions in the school are a cover for their true roles, or they're hiding secrets about themselves, including having deadly supernatural powers. Are you sure you really know them, or just who they're pretending to be?
Periphery Demographic: Aside from the normal lovers of Magical Girl series, Mai-HiME gained a surprising amount of interest from lesbians, mostly thanks to the draw of the Natsuki x Shizuru pairing. This was embraced by the writers, and expanded upon in the supplemental materials, and then made canon in Mai-Otome, along with various other couples and hinted same-sex crushes.
Real Women Never Wear Dresses: Fans have accused Akira of Chickification for wearing girlier clothes towards the end of the story (in the manga, there's a scene in the ending in which she's trying on a girl's middle school uniform). Not only it ignores that several of the HiMe are actually rather feminine girls (Shizuru is a Lady of War, Natsuki is a Gunslinger who wears her hair very long and loves collecting lingerie, Mai herself is kinda motherly and a Supreme Chef, etc.), but also "forget" that the main reason Akira dressed up as a guy is that she was trying to hide the fact that she was a HiMe in the first place, thus she started wearing skirts only when her mission was over and she had no real reason to hide her gender. Girliness Upgrade, yeah; Chickification, uhm, no.
Interestingly enough, Akira is still using the highly masculine "ore" to refer to herself.
Replacement Scrappy: Another criticism of Haruka being a Hime in the manga is that she is one instead of Shizuru.
What an Idiot: Yuuichi. His attraction to Mai becomes increasingly obvious halfway through the story, and while his desire to help is commendable, he breaks his promises to Shiho twice in doing so, eventually leading her to attack Mai after Nagi manipulates her some more.
Akane, especially considering her mental breakdown after the death of her boyfriend, Kazuya.
Mai. She blames herself for a childhood tragedy in which her mother died and her brother's heart was weakened. She's forced to fight against her friends in the Carnival, and loses two of her most important people. The toll these tragedies take on her becomes increasingly evident over time.
They Wasted a Perfectly Good Plot: A dark and tragic universe where Magical Girls are given their powers as part of some Satanic ritual and are forced to kill each other to protect the ones they love could have made for an amazing story... if it had actually started with that plot instead of having it randomly hijack a completely different show after nearly two-thirds of the episodes had been carefully built up as a scientific deconstruction of the Magical Girl genre. Sunrise themselves apparently agreed with this assessment, considering they made EXA.
Woobie Destroyer of Worlds with shades of Freudian Excuse: (manga) Takumi's justification for his actions as host of the Obsidian Lord was that a world that has brought him absolutely nothing but suffering wasn't worth preserving.
Considering he was a corpse when Obsidian Lord assimilated him, it's not like he had much of a choice in the matter.