Here's an idea.

A change to the usual "The world thinks Harry's sibling is the ___-who-lived, but Harry really is" idea. Here's the twist. Both siblings know of it, and it was Harry's idea.

General idea is, Harry and his sister were older when the whole thing happened, but it was clear to Harry that his sister had little to no magical power. So, he says she is the girl who lived, because he knows the world will basically hand everything on a platter to the person who rid the world of voldemort, and he can make his own way.

An alteration could have the usual ages and timeline, but after the years with the dursleys and so on, harry has taken a protective streak of her. he tells the press, foregoing dumbledore, that it was really his sister, so they embrace her existence most.

She holds a lot of guilt that the world ignores/hates harry, but has to go along with it to cover her own deficiencies.

This could be taken on in many ways, hell, someone could make a incest story out of it all if they wanted to, just a random idea I got that could be toyed with since I'm sick of the "cocky sibling who didnt do shit but revels in the attention" kinda thing.

Be nice for a change is all. Well, lemme know if anyone thinks about taking it up, im playing around with trying it out, but I have a lot on my plate now.

 

While I'm sure this idea has been done before somewhere (not with the incest, as far as I can recall), it hasn't been done too much and is much better than the arrogant!fake!BWL storyline most of these stories tend to go on.

The only problem I see with it is that Harry would almost certainly be portrayed as the super smart, Slytherin, manipulator Demi-God in the hands of an unskilled author. That's not good, children shouldn't have a reason to lie about something like that - it'd especially effect the younger sister (how old would they be when it happened?) since children with protective older siblings don't tend to mature before they hit secondary school.

Aekiel

EDIT: Oh, and this belongs in the challenge section.

 

Also, They'd have to be considerably older to even be able to perceive of the amount of lavishment the etc.-who-lived would get--a young child has little perception of that sort of thing. I would rather suggest something along the lines of Dumbledore approaching them as small children and convincing them that it needs to be a secret that harry is the bwl, and stresses the importance of his sister being the gwl, for example. you can have anyone come along that you want instead of dumbledore, but it seems like something that canon!dumbledore would do--and, then nurture both children and make sure that they both have what they need.

 

Well considering the world post-voldemort, i figure, would be quite calm for the years when he is completely out of the picture, with death eaters not out for revenge as they are trying to set up their cases of imperius and so on, i don't think it would be extreme danger.
As for the scar, it could be an interesting look into the darkness of Harry, or his commitment to helping by any means necessary, you could potentially have him cut a scar onto his sister's head as well. or for that matter, try and see how it is the world knew he had a scar when the story was supposed to be kept quiet. Maybe Hagrid felt the need to keep his mouth silent from telling drunken stories of finding Harry, if there was more than one life in the balance, or something were to happen to him upon finding them. Maybe the world doesn't know about the scar in the first place? Be an interesting thing to poke around with, if the Boy/Girl-Who-Lived didn't have some clear defining mark for the world to gape at.
It has a lot of kinks and wholes in the planning where things could be slightly different and make a whole new story, but i figure, if Harry had to grow up looking out for someone else as well as himself, and not just himself, he could have become a completely different person. Having to watch out for a much more fragile girl as well as himself could bring out a side of Harry that was lost when he let the Dursleys beat up on him with no actual resistance outside of running. Could explain things he does later in life, however, I wouldn't see this Harry being in Slytherin just because of the fact that his sister may not be there either, and he'd want to be in a position to look out for her. Maybe both end up in Ravenclaw, Harry because of his intelligence and ruthlessness in the name of knowledge, and his sister because theory and reading is all she can do in magic well and consistantly.
Hell, could be they both end up in Hufflepuff and cause a revamp and revolution in the world's thinking of the 'puffs for all we know. Bunch of ideas to play with in the basic "world" of this idea, up to anyone to mess with it.