This series has a lot of sentimental value to me. I read the majority of it in a fragile period of my adolescence, mostly in a graveyard across from my high school while skipping class after checking out each new volume from the library. It has such a strong place in this formative phase of my life; picking up any of the volumes brings me right back to that graveyard (which, contrary to common expectation, is a very nice place to read), and I can remember how I felt when I read them there. I really felt like these characters were my friends.
Though it is ultimately a romantic comedy series, I always detected something distinctly melancholy underneath the lighthearted proceedings. Let me be clear, I am a very characteristically sad person. I've never been good at making friends and I've never been happy with my circumstances, always feeling that I will never measure up to anything; that life is happening elsewhere. So really I found a home and friendship with these characters that felt very special, but I also knew that it couldn't last. The latter volumes of the series left me with the sinking feeling that this was all falling apart, like I knew that it would from the beginning. "This isn't how it's supposed to happen" I would find myself saying into the pages. I felt frustrated that these characters weren't feeling the way they were supposed to, deviating from their original relationships and, maturing in that irreversible way that I saw my own friends maturing before me.
[Note that this next part will have slight spoilers for the full series]
Ultimately, this series started out being about these deeply aloof and socially inept characters finding a home in their friends. It became a story about being forced to grow up in an adult world that has no place for sentimentality and such deep connections through friendship. I found it getting more painful to read as it began reflecting things happening in my own life that I didn't want to happen.
Increasingly, during the final years of my education, I was finding out how flimsy these friendships I had formed with people really were. Friendship has always been the most important thing to me, and it hurt finding out that most people simply do not value other people in the same way. Humans are constantly changing, and they will never be exactly who you want, or have come to expect them to be.
That's why was frustrated when the characters started focusing on romantic relationships and neglecting the friends that depended on them to be there. I was angry when Haruhi made the decision to leave her friends and study abroad, because all this is what I saw my friends doing in real life, and I was angry at them for leaving me behind. But, this is the way our world works. The characters of Ouran have to make the same decisions that everyone their age has to make, at an age when they aren't ready to make them. Regardless of nationality or country of origin, ours is a society of increasing superficial connectivity, and one of deepening isolation on an individual level. We all feel really alone, and we all really want somewhere to belong and someone to belong to. This is what Ouran ultimately explores. It's hidden behind a shoujo label, but it's there, because I felt it.