When Steven Spielberg was making Raiders of the Lost Ark and the other Indiana Jones films he pulled from many B grade adventure movies he saw in his youth. The first three of Indie's adventures take place in the 1930 s because most of the B movies made then were adventure films like Tarzan the Ape Man. In making the Indiana Jones films, he showed that B-movies, for all their camp and cheesiness, could be great given the budget and talent of an A-grade movie. Likewise, by making the Monogatari series, NisiOisiN and Akiyuki Shinbou somehow managed to extract the potential locked deep within the harem genre.
But Usny, you argue, harems are mediocre at best despite frequently being loaded with famous voice actresses that play hot as fuck girls who are the only reason anyone ever watches those shows; the Monogatari series couldn't possibly be a harem. Let's go through the list of common harem traits, shall we?
High school setting: check.
Average main character: check (in Kizumonogatari anyway).
Surrounded by girls that each embody a certain archetype: check.
They all want on his nuts: check.
Gratuitous fan service: definitely check.
Survey says harem.
That's where things get interesting. Most harems are systematically designed and executed to tease the audience with things they want, whether it's physical fan service or making the audience want to vicariously pursue a certain girl. Physical fan service is easy to deliver on, though most of the time it stops short because a lot of harem anime has to be TV friendly. Shipping fan service is more fickle because the show has to appeal to more than one girl's fan base, so the most we usually get is a short arc that attempts to humanize each girl so we can sympathize with them. In Rosario+Vampire, this means things like introducing Mizore's family and showing that if Tsukune doesn't get with her, she'll be forced into an arranged marriage. In Bakemonogatari and the subsequent novels, this means overcoming supernatural beings that symbolize psychological complexes.
And a lot of head tilting.
Hitagi's past is significantly traumatic given the horrible experience of almost being raped and the pain of her family's subsequent rupture. That is a terrible thing for a young girl to bear and it is no surprise that when given the opportunity to offload that anguish, she would take it. Repressing the pain does not fix the problem though, it merely hides it. This is manifested in Hitagi's missing weight. Part of her is literally missing because she does not want to face it. This is the irony of many victims who end up being defined by their trauma. The trick to getting over something is not to run away from it, but to face it head on. Therapists know this and guide their patients to the problem and through the process of getting over it. In that sense, Koyomi and Meme represent the therapist. With their guidance, Hitagi physically (and mentally) prepares for an exorcism that she ultimately conducts on herself. She faces the pain and memories she was hiding from and, in accepting them, becomes whole again.
Hanekawa's imperative is to be a paragon of perfection, whether she consciously does it or not. It is impossible for a human, inherently flawed as we are, to embody this ideal, but Hanekawa tries nonetheless. First, she deals with that pesky thing called stress by hijacking an oddity that tried to futilely possess her. Then she outsources her jealousy towards Koyomi and Hitagi's relationship by producing a new oddity entirely. This is very similar to how people with Dissociative Identity Disorder produce entirely new personalities in the face of severe physical, sexual, and psychological abuse in order to shield themselves from future trauma. As a result, Hanekawa appears superficial and incomplete as a character until her arc is resolved in Nekomonogatari White because she tries to escape from the negative aspects of herself. In the end, Hanekawa has to risk failure and confess to Koyomi. Even though she is rejected, she is able reabsorb the oddities she produced because the catharsis allows her to accept her imperfections.
Nadeko's deal is all about the give and take of privilege. Shinobu says it best when she tells Nadeko how it must be nice to be so cute that she can depend on everyone to do everything for her. From that standpoint, her cuteness frees her from responsibility because Koyomi will always save her or teachers will always excuse her for not doing her work because she's meek. There is always another side to privilege, though. In Bakemonogatari, she rejects a classmate who has a crush on her, resulting in that person and the person that was crushing on them cursing Nadeko. The snakes she is cursed with literally strangle her, not unlike how she is stifled by the prerequisites of her privilege. In order to maintain one's privilege, one has to keep up appearances and be constantly judged by others. It is not until Tsukihi cuts Nadeko's bangs and robs her of her cute privilege that Nadeko is free. Relieved of the need to maintain a cute, meek persona, she proceeds to outwardly vent the frustration she was forced to hide from the people around her. To that end, Nadeko's hallucinations about the white snakes resulted in her escaping a cage wrought by social expectations and led her to assuming enough power that her lost privilege is rendered trivial.
I could go on, but those three are my favorite because of how seamlessly Nisio works the symbolism into a narrative that fits the "boy meets a bunch of girls" premise that the harem genre is founded on. Out of tsundere, class rep meganekko, and imouto characters comes commentary on overcoming abuse, the dangers of perfectionism, and struggling with socially enforced roles.
Of course, the series wouldn't be complete without the narrative catalyst that is Araragi Koyomi. He already blows every other harem lead in anime history out of the water by having an entertaining personality instead of being the typical blank slate male lead for the (apparently bland) audience to project onto. Not only that, he does something that is completely alien to most anime males: he commits to one of the girls. Unheard of. He's arguably the most like his fellow harem leads in Kizumonogatari when he's a friendless loser who is only just realizing how to turn the swag dial up, but even in that rudimentary state, he almost bangs Hanekawa in the school storage shed. The man is unmatched.
Cue Carl Sagan
The writing and characters alone are enough to be impressive; combine those with Shinbou's unique and absolutely sublime visuals and Monogatari becomes overwhelmingly good. Anime tends to pretend like its characters live in a bigger world by having stock background characters. Shinbou abandons this pretense and strips the world of everyone besides the people the players in the given scene and sets their meandering dialogues to grandiose and gorgeous backdrops and architectures that would make Frank Lloyd Wright cry himself to sleep every night.
It is a testament to the talents of Nisio and Shinbou that they can construct such rich and artful work within the framework of a genre that is inherently about cheap gratification. Like Spielberg, they excel at pushing the envelope and producing fantastic works in the process. The have proven that there is no such thing as a bad genre, only bad titles. Whether their level of talent is Spielberg tier is debatable. That honor would probably belong to whoever makes the Indiana Jones of hentai.