Is there a manga with the female protagonist having a bad ass kind of character. Almost as if she was in a gang kind of thing but doesn't have to be.
Basically the opposite of common shoujo characters. Not the energetic or nice type but one with a dark side yet not depressing if you know what I mean.

Yamato Nadeshiko Shichihenge - You might consider her personality depressing, but it's a pretty funny manga. Unfortunately it's very episodic and incomplete.

Gokusen (josel) - Yakuza heiress. I don't know if I would describe her personality as dark per se, but she's very awesome and kicks ass.

Then I can think of a few split personality stories - Othello (Ikezawa Satomi) and Akuma de Junai.

Kechonpa in a way

Present wa Shinju
Oresama Teacher
Lingerie
Lady Detective
Fujoshi Kanojo

I don't think "shoujo" and "dark side" and "not depressing" and "good" go together, but I've tried my best. I think I'm interpreting dark side too liberally so if you could clarify that'd be great.

Elitism? If I am not elite, then who is?

Tokyo Crazy Paradise - she's a tough fighter and is sort of in a gang

The Kidnapping of Minja Jo's Boyfriend

Yuyu from Nanairo Kakumei. Well, she is not the protagonist actually, but she really dominating the story.