Late for the party, but I just HAD to add those:
You need to read Fruits Basket. The heroine at first glance seems the typical shoujo heroine. She's ditzy, a pushover, and cheerful. But...As the story progresses, you realize how strong she is. There is a huge cast of characters, and they're ALL flawed.

Tonari No Kaibutsu-kun: This one was pretty good. Again, all characters are flawed. The stoy starts off a bit weird, and the characters seem a bit too quirky at first, but I actually found myself relate to them, and I liked how they were all different. They weren't the typical 'good' characters, and in fact some of them had bad personalities, but I really liked how they were shown as supportive characters instead of antagonists. I don't know, I just loved this manga a lot.

HORIMIYA IS A MUST: This one is just....so realistic. The interactions are very natural, and the characters all have their strengths and weaknesses. The heroine is a bit mean and selfish, but she does care about her loved ones. I liked that. The guy is too much of a sweetheart, but he also has his mean side as well. There is also a lot of focus over the side characters.

MOUSOU SHOUJO OTAKU-KEI IS A MUST TOO! It is seinen, but I didn't really notice that at all since it seemed like a non-cliche shoujo. The romance is VERY realistic, and the characters have a lot of depth
AS FOR THE HEAVY ONES:
Six Half: it is so original. Really. And very interesting. It is more about moving on and finding second chances.

If you don't mind BL, I will have to recommend a lot of things too. Those are some of my favorites:

Super Lovers: it felt to natural and the characters are so complex. It is more than it seems, and the characters have a lot of depth in them.

• original, atypical manga that doesn't use the same old tropes of manga
• romance with two realistic characters, not just "manga characters"

14-sai no Koi


Well, I think it has all of what you want, but there is no scanlation yet
atypical : focus more at another form of true friendship
intelligent : deep and twisted characters
realistic romance : well, it's realistic enough, the helped girl slowly fall in love with the boy who help her naturally but not dependent to him
Nanairo Kakumei

Fushigi na Shounen
Tamashii no Futago
both of these are original, atypical, and really, really good

I look for three of these types of manga constantly. Here are some great ones.

Yokohama Kaidashi Kikou
http://www.mangaupdates.com/series.html?id=586

My Lovely Ghost KANA
http://www.mangaupdates.com/series.html?id=7530

Noramimi [cute, charming, quietly moving, absolutely unique]
http://www.mangaupdates.com/series.html?id=7530

The Music of Marie
http://www.mangaupdates.com/series.html?id=1564

NoragamiWhile the first two chapters are fairly big duds after that it goes on to become a complex manga about the nature of family, toxic relationships, and abusive parents; all the while managing to somehow not give in to despair. The female lead is unique in that more than being a romantic partner she represents Yato's (the MC's) happy place. The place he can go to when life starts to get too much for him to handle. I could go on and on about what makes said series great but I do not want to spoil it for you.

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http://fightingdreamersscanlations.wordpress.com/

Omoide Emanon - If you want pretentiously intelligent discussions about life and the universe and atypical characters, here you go. It has romance too, not sure if it's the kind you're looking for though.

Shoukoku no Altair - Because you said you liked Chang ge Xing/Choukakou. It has practically zero romance, but if you're into the whole intelligent war strategies thing, give it a go. And the art is nice.

Umi no Cradle - I am putting this here because I partly just want to share this manga to the world. The art is gorgeous, and the characters have plenty of room to grow. It's just starting out but it doesn't follow the typical manga formula. If you ask me, the storytelling follows a more western novel type.

Olimpos - Pretentious, almost to the point of being philosophical, I suppose. There's barely any romance, as far as I can remember though.