Spoiler'd: Unhelpful
Hmm, I love Tokyo Crazy Paradise and would also recommend it, but it's not told so much by a sidekick's point of view. She's technically the sidekick, since she's a mafia boss' bodyguard, even though she's actually more badass. Though technically she could be considered a tragic hero, she acts like a boke most of the time.
The the art is lacking (well, Nakamura's current artwork in Skip Beat and her stories more than make up for it), but the story is absolutely amazing~
Spoiler (mouse over to view) Hana ni Arashi is a shoujo manga, and doesn't fit many of the criteria except being overwhelmingly physically powerful.
I second Yanki-kun to Megane-chan, though it's a gag manga.
Spoiler (mouse over to view) Durarara!! has similar elements of a protagonist that is otherworldly, and she is powerful. (There are many characters with large roles, so it's not told in her point of view very often. I recommend either the anime or the novels. The manga is, um... Lacking.) But the story is much more focused on dramatic elements. But look into it if you'd like. Shinshi Doumei Cross is also a shoujo manga, but the main character is pretty much a super-powerful ex-delinquent. It's very well written, but not much shounen-mangaesque focus. Pandora Hearts kind of fits, but it's likely not what you're looking for. She's no hero.
I haven't read Girls of the Wild's yet, but it seems to fit quite well (note: manhua, but has a great rating it seems).
Sorry there are so few titles I know for this request. :C
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