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Here's the thing. Suppose I wrote a Strawberry Panic! fanfiction. I created a new character that was the child of a famous and spectacular Étoile. This new character is amazingly beautiful, very pure, with excellent booksmarts, excels wildly at sports, and is modest to boot. That character joins the cast as an exchange student and instantly becomes the most popular character at school with many of the cast falling in love with the new character. One of the candidates for the Étoile even agrees to step aside for this new wonderful new character. The election for the Étoile is only in a few days but the new character wins handily. Suppose I'm a guy and in order to make this character more of an Author Avatar, I make this character a Wholesome Crossdresser. Well, wouldn't you say I've just made a huge Mary Sue or Marty Stu character? Well truthfully, I am describing a Mary Sue or Marty Stu style fanfic. Unfortunately, I am also describing the plot to Otome wa Boku ni Koishiteru.
I dunno, I guess there's just something people find hilarious in the idea of the absolute embodiment of feminine beauty/virtue/wossname happening to be male.
Possibly, but that can be a one time gag, not something to base a series on. It probably doesn't help that Mizuho is also made out to be the embodiment of the masculine ideals of chivalry, honour, and physical skills.
The 'series' was originally a porn game. It's possible for them to be well written, but not necessarily a top priority for the creators. In this case, I don't think there's really any way to make this series not be a self-insertion Marty Stue plotline without completely reworking it.
In a way Otoboku's Mizuho is a subversion of some of the genre's rather unwholesome characters *Cough*Makoto *Cough*School Days.
His academics are very hardly brought in (unlike most Mary Sue cases, in which they constantly remind you), and hes said to be a decent athlete because he's a man (whether this is real or not in real life is of no importance). Furthermore, most of those characteristics are obtained after 12 episodes of Character Development (and mostly through friendship!), something most fanfics dont have. Also, a very girly man getting the position of Etoile is not less pompous than a girl getting it. Its supposed to be an idealistic show.
I've watched the entire series, and I feel like you're confusing perception with fact:
"excels wildly at sports" is not true, it was gossip blown out of proportion. (At my old high school, the shot that started this rumor would be normal, and compared to Mariya, Mizuho would be much better, helping the rumor to spread).
"with excellent book-smarts"... He never show any anything above average intelligence to me; I know people that got degrees without revision. Takako states in one of their early meetings that (s)he must be intelligent to have passed the entrance exam, without prep work; this is entirely assumed.
"very pure" as in a pure maiden took 5 episodes (it was still arguable) with the help of 3 girls, one of which was exactly what he was after. His screw-up in the first episode was noticeable.
"amazingly beautiful"; while our opinions may differ, I think 2 or 3 girls were better looking.
"many of the cast falling in love"; it was just 3 girls; Takako, Mariya and Ichiko. The student body had cruses on 'her' mixed with admiration and fascination, but remember the setting - private schools like this are often isolated with everyone/thing on a single campus. Transfers are almost nonexistent, as are visitors and chances to go off campus. The gossip is greatly amplified, and Mizuho was the only new thing (and he kept breeding new gossip). Add the most popular girl being his friend, and that clarifies why he's sought after, not necessarily romantically, but for popularity.
The martial arts were actually like green belt level.
In the VN, at least, Mizuho was referred to as having been top of the class at his previous school, a school that, when name dropped, caused several characters to question why he'd leave such a prestigious place to come to Seio. It also explicitly mentions, more than once, that he was further ahead in all of his classes at that school than the corresponding class at Seio was. It's fairly well established that he's, at worst, a big fish in a small pond at Seio.