I'm currently searching for Mangas, where the MC rarely uses his true strength (like said in the title 😀 ) instead only uses parts of it. I don't care for the reason, it could be because he wants to hide it or because he doesn't want to use it, or something else.
The first examples that come to my mind are Blood Lad and Nanatsu no Taizai.
I'd be grateful for good results.

Maoyuu Maou Yuusha - "Kono Watashi no Mono Tonare, Yuusha yo" "Kotowaru!" and "Gun x Clover" comes to mind.

Mahouka Koukou no Rettousei
Tora Kiss - a school odyssey
Seirei tsukai no kenbu (manga only got few chapter, so I'd recommend the LN)
Id
Tripeace (due to memory loss but regains them after around 20 chapter or so; gender bender quite a lot (mc crossdressing to hide identity))
Crimson Grave
Hagure Yuusha no Kichiku Bigaku
Seikoku no Ryuu Kishi (maybe, not sure anymore)
Beelzebub

Noblesse Both leads hide their true strength.....well, it's more like they don't find a reason.

[img]http://media.tumblr.com/e43f35cfdd762cc666571a6dd0f163d5/tumblr_inline_mhbel8Cy8V1qz4rgp.gif[/img]

Chrno Crusade because his powers shorten Rosette's lifespan.

What I like in Trivial Pursuit style. Pick your category:[img]http://i379.photobucket.com/albums/oo233/Reid4891/Manga/trivia-1.jpg[/img]

Take a look at this topic: http://www.mangaupdates.com/showtopic.php?tid=39804&hl=pretending

@mevan883 MC may be pretending, but he actually uses his strength quite often just hides it
@Jidan Mahouka Koukou no Rettousei, Crimson Grave, ID and Beelzebub fit really well, too bad i already read them
@strixflash Noblesse would have been a good Example, but somehow i forgot it...
@reid1 i didn't read it yet, but maybe now ill do it that souds like it would be fitting, thanks !
@nolanfa i don't want a MC who pretends, but someone who just doesn't use his real strength often, for whatever reaason

NOblesse is spot on

Medaka Box maybe?
http://www.mangaupdates.com/series.html?id=40888

Yeah, just me, your every day person with a computer.
And a brain.
Well at least I think I do.

@ scytherman:
well, if they pretend not to be strong, obviously they won't use their real strength often. The two topics are different, sure, but they overlap.
So I still think you should check it out; moreover most of the mangas people indicated here are on that other topic as well.

The Ruler of the land - MC is genius and can copy any martial arts shown to him, but the one he uses is the air step (run faster and stuff) to run away because he doesn't like fighting and would rather perv on girls