In many light novels/manga, the lead ends up with the obvious girl, the tsundere that anyone could have predicted from chapter 1. Ex. Love Hina - Naru.
Are there any romance where the girl isn't so? Asura Cryin' is an imperfect example, MM! is another.
Especially if the girl is manipulative, dominant even, having the "ara ara" feel, where they seem to have everything under control, and know more than the main character could hope to know. Sort of like older Mikuru from Haruhi.

Are you looking for:

a) manga where the MC ends up with a girl who is not the main female lead?

or

b) manga where the main female lead is not the typical tsundere, neurotic, hapless, hothead?

Because suggestions for a) are few and far between and the mere act of suggesting them would ruin the non-stereotypical nature of them, such as:

Ichigo 100%

But I can suggest a few for b) (happy-ish, non-ambiguous endings only):
Ai yori Aoshi
Ashita Dorobou
Hoshi no Samidare
Kanojo wa Sore o Gaman Dekinai
Koharu no Hibi
Mirai Nikki
Orange Yane no Chiisana Ie maybe, been a while since I read it
Psyren somewhat
Shingetsutan Tsukihime
Tasogare Otome x Amnesia

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