I am looking for the protagonist to have something special/unusual about him. I know very well that there are many series like that. But I am looking for the protagonist (whether he/she know or not) to have or be something different than everybody else, and the readers don't know what that something is until later on in the series. The reader finds out about that something through hints here or there, or the author tells us out later on. but I don't want to find out right away.

-don't care about settings, genre (except hentai/yuri/shounen ai), or length of the series
-I would prefer a fantasy/supernatural/sci-fi feeling, but if it is a good series I don't care
-no rushed endings
- can be an add on, like if the protagonist is already different but then something else gets added to the character
-also if you have a series that doesn't fit exactly but sounds like something i might like, don't be afraid to share

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"They were traps? I thought they were attractions"
Killua (Hunter X Hunter)

I think, seikirei, and freezing fit your discription. And don't forget Aiki, it's not sci-fi but martial art tough.

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"I already decided I'll do it, so even if I die fighting for that cause, that's fine with me."
"Who the hell do you think I am?!"

Mirai Nikki (Yuno) exactly fits your request.
About something that doesn't fit exactly (mostly because the revelation is not very late in the story) I'd say you could try Hekikai no AiON or maybe Gosick.

Also I feel like to mention that all the characters in question are main characters imho but they're not the person which from whose point of view the story is told (similarly to Sankarea where the "special" person is Rea, not Furuya, for example. If you needed the special person to be the guy who is telling the story the closest thing I can think of is probably Magi).

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What I like in Trivial Pursuit style. Pick your category:

i second Magi seems like a perfect fit

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"I don't know everything, I'm just really good at explaining the past, so it seems like I know everything"

The Breaker... again.... ~__~
I feel as if i have only been recommending this one manga (manhwa) only.... for as long as i can remember....
But oh well... regarding the topic.... umm... the protagonist... is as good as a twig... and he somehow gets into some extra-ordinary circumstances... the usual shounen.... BUT... well... it has been hinted all along that he might have something very special indeed... but its yet to be revealed... the breaker is now in its seconds season... (the new waves)... and now the hints are getting more obvious... sorta... unless its my own imagination...

Anyways... its still definitely worth a try...

I also forgot about Suzumiya Haruhi no Yuutsu but I think you should try the novel instead of the manga if you start it.

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What I like in Trivial Pursuit style. Pick your category:

Siesta

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（・◇・）/~~~ ♥

Iris Zero, LOL!!!

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Nuff said.