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You see, when you reading mangas, main charcter become your favorite character, but sometimes your favorite character can be other than main character who is friend-companion of main charcter or even enemy of the main charcter, and sometimes you dislike main charcter which probably make you dissapointed at the end of the series.

So what mangas which main character become your fav and which mangas you didnt like main character or someone other than main charcter become your favorite and why?
As for me:

I agree with guts with berserk. And A manga I read randomly is Black Cat: Eve would be my favorite, train isn't that interesting.

For most of them I also like the main, not just as much.

Air Gear - Kilik. But I don't hate the main at all. Ikki and Ringo are just my third and fifth favorite, that's all.
Kuroko no Basket - Aomine, because he has the type of basketball I love the most. Also I like his chara-design and I love his arrogance because there is a reason behind it.
Medaka Box - Anshin'in. Since I hate Medaka, not particulary like Zenkichi, dislike Kouki and don't give a damn about Kikaijima…
Shaman King - Asakura Hao and Yoh. So I love both the protagonist and antagonist.
The Breaker - So Chun Hyuk, better design, better personality, fighting style.

I've only read one manga so far where the main character was my favourite (other than Lucky Star which hardly counts as I only looked at it because of the anime and hardly actually read any), and that's Watashi ga Motenai no wa Dou Kangaetemo Omaera ga Warui! - which has such a small cast of noticeable characters that it doesn't really count.

Then again I haven't read all that much manga so it could just be a total coincidence.

Btooom! - ryouta - he knows his own weaknesses and tries to seek self-improvement

Groove Adventure Rave - Haru - basically everything you want from a shounen male protagonist: determination, conviction, intelligence, laid-back attitude, and protecting his important person. He does this without being over the board or looking retarded.

Well, Ryo Saeba, it's no very original but he is a very handsome,gentle,smart,human, all the qualities of a man. But a very sad man with no past.

Gintoki and Hijikata from Gintama
and
Roronoa Zoro - One piece i really adore him!

Except for Onizuka in Great Teacher Onizuka, there's almost always somebody besides the main character that I like better.