OK I'm looking for a Shoenen/Seinen type manga where the main character gets in a relationship at the beginning or middle of the story as a confirmed couple.
I don't want the relationship to be the main focus of the manga, I want something like "Save the world and found myself a girlfriend while I was at it."
Mangas that fit are Watashi no Messiah-sama and Flame of Recca the latter only loosely fits (and I can't quite remember if Rave_ has this I think it does).
I absolutely don't want it to be "And they became a couple... THE END." or a one chapter after story, I want them to get together a build their relationship over the course of the main story.

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What you fear more is the only difference.
Positive decisions are made in fear negative consequences,
Negitive decisions are made in fear of positive decisions not giving the outcome you want.
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Greed is the fear of having too little.

Demonblaze0's personal thoughts

kare kano the beginning of their relationship is only the first volume! all other 20 consist of their progress. Thou is shojou.... sorry, it was the only thing I could think about

Judging by the manga you listed, I assume you want some some sort of action going on instead of the relationships being the key focus of the story.

Magico (IWAMOTO Naoki)
Itsuka Tenma no Kuro Usagi
Mysterious Girlfriend X (not action, sorry)

Not exactly what you want but pretty close.

psyren

Hoshi no Samidare

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I like your anti-cliched requests pal and here is what I recommend:
Eureka Seven Not sure about this one since i haven't read it myself
Gantz Here the relationship plays a part in the plot as well
Zennou no Noa One of my personal favorites. Just to give you an idea think of someone like lelouche from code geass or light from death note getting a girlfriend!
The Breaker Don't know if it fits cause the hero isn't the one getting a girlfriend but still it's pretty good (and there are hints of the hero getting a girl but that's about it).

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Out of all of these Outlanders is perfect.
Hoshi no Samidare fits a little bit but not quite because they didn't become a couple until the very end.
The rest don't fit or the relationships are too vague. (except Magico (IWAMOTO Naoki) I haven't read any of that so I can't judge it yet)

________________
All choices are made in fear,
What you fear more is the only difference.
Positive decisions are made in fear negative consequences,
Negitive decisions are made in fear of positive decisions not giving the outcome you want.
Embarrassment is the fear of people knowing your real thoughts.
Greed is the fear of having too little.

Demonblaze0's personal thoughts