At first I felt guilty for reading this manga. The anime adaptation didn't help this feeling either, capitalizing on all the fan-service and "loli" theme; didn't help that feeling of guilty, too, that this series got translated by a guy that receives comissions for working on hentai (mainly on lolicon and worse material) and that I had to get out of my way and lurk around dark places to read it. But, against all the odds and feelings of discomfort over those years, I continued to get the scanlations for this tale that screams "truth" and "change" all over the place, like the best novels and dramas that are out there.
This series is taboo, yes - but it isn't as cheesy as, say, Oreimo and isn't, for the most part, played for laughs or manga and anime stereotypes (even if those are, sadly, present); this series has nudity and sexual innuendo but, at the same time, questions the very reasons that make us erase those topics from child upbringing - be it at school or at home - and end up leaving room for the emergence of bigger problems.
"Children are people too, so they also have desire, and end up wanting to know love and to experience carnal feelings". This manga throws this sort of inconvenient truth at our faces at each page, while questioning the processes that end up hurting adults on the long term. No chapter can be taken out of context for that matter, and a careful / open-minded read is necessary to truly grasp the authors intentions.
... and, well: Don't forget that the author is a woman. More than once, to my dismay, girls told me things like "the first time I fell in love I was 9 years old", or "the first time I really liked someone I was 12" with the most straight face, like it is completely normal; this was in real life, and the one shocked was me, not those girls. Those children, now women in their mid twenties, are not sick nor crazy, and there is nothing to be so shocked about children growing up: Sick is a society that doesn't want to discuss those "inconvenient" topics, that doesn't want to see it... and that gives space for those who abuse those children's naive desires and dreams. Series that treat those topics superficially or "for laughs" end up reaching cult status, while reading something like "Kodomo no Jikan" can actually make random people accuse you of being a pedophile.
... Well, I'm glad that there are people with enough disposition to go out of their ways and give us such touching, awe inspiring and mind changing stories - even if this sick industry asks for loli fanservice in order to boost sales.
And about the ending,
... it wasn't to my taste, yes, but neither was the ending for, say, Koi Kaze; The ending was "happy" if you look from some characters points of view, even if the "guardians of all that is sacred" (read: haters that commented before me) think of it as an abomination. Oh, and there was a timeskip that made all that stuff somewhat valid: If you are the kind of people that goes all "Naru X Hina" or other silly stuff, know that the protagonists are then older than said Naruto - so... yeah.