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.
YMMV: Kodomo no Omocha
Awesome Music: Sana's Raps. The rhyming of some of them are just random, but they are catchy.
Die for Our Ship: Being a middle schooler doesn't protect Fuuka from being bashed heavily by Sana/Akito fangirls. Naozumi isn't exactly liked, either.
Yokooh No: In-universe example when Sana is attacked by Naozumi's fangirls, and they even break her leg!
Unfortunate Implications: For some people, the anime's handling of Sana's origins and specially both Misako slapping Keiko and calling her borderline abusive names and the time when Sana's Disappeared Dad showed up was... tasteless.
What Do You Mean, It's for Kids?: The manga was published by shoujo magazine Ribon, but it has a lot of dark moments, beginning with the whole scene of Akito asking to Sana to kill him. It also deals with teen pregnancy (Sana's biological mother was pregnant at thirteen years old... and it is implied her own uncle raped her), abusive parents (Tsuyoshi's dad), and Sex as Rite-of-Passage (Sana and Akito plan to have sex in a very misguided attempt to stay together).
The Mizu no Yakata movie itself (being filmed in one of the arcs of the series and later adapted into a whole volume itself) also manages dark tones (drugs, being one of them), something that Obana would explore later in her more mature works as Partner and Honey Bitter.
It makes you wonder why the last arc of the anime tried to be a tamed version of the almost final arc of the manga. It dealt with a lot of drama and darker tones compared to the first volumes for an anime series generally aimed to kids in Japan...