It's hard to explain, but a lot of Yoneda Kou's work would fit in this. I'm looking for a yaoi that isn't specifically about One couple, more about.. the uke. where we can see his life, or the plot isn't All about him and the seme getting together. You know what I mean?
I also really like yaoi where they live in the slums/ghetto, something like Acid Town or alike c:
suggestions will be adored~

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http://www.smackjeeves.com/comicprofile.php?id=135230
yaoi webcomic ._.

Hmm I recommend New York New York, well obviously it's about the couple, but it's not just your everyday yaoi where the story is just how the got together and after that. It's more about the problems they go through as they're together and you'll see the dark past behind the uke too.
Also Cut, though both uke and seme got issues here but it still counts.
And defenitely Saezuru Tori wa Habatakanai!! It fits perfectly into your description.

I'll edit more if I remember later ^.^

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K n e e l .... This is the difference between your and my eye-level.
Rai from Noblesse

thank you, sadly I've read all of those but if you Can suggest more, that'd be super ^^

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yaoi webcomic ._.

Zankoku na Kami ga Shihai Suru
Jin to Neko wa Yobu to Konai
Border not sure tho