Theory could celestia actually not be lunas sister

[Cannon and rarity 38]

see celestia nad luna look nothing alike  :comeatus: see look at that and this (couldnt find a celestia face) and there personality they have nothing alike they could of forgot everything about them and they were jsut best friends but then jsut forgot and thoguht they were sister anyone if you do reply to me 

[Odyssey 5,713]

Uh... it has been stated repeatedly that Celestia and Luna are sisters. If Celestia's grief for banishing Luna to the moon, Luna's feelings on how it feels to be overshadowed by her elder sister as well as other little things like The Journal of the Two Sisters is not enough evidence, then I don't know what is.

 

Just because they don't look alike doesn't excuse it either. At least they share constant flowing manes and have the magic that can raise planets. Those two abilities seem like they're similar genetically. As for personality, we don't know much of it, other than both are kind rulers. Luna's more mischievous, but so is Celestia at times.

Edited March 28, 2015 by Odyssey

[Ashen Pathfinder 16,151]

Well, in the end, the Cake twins look nothing alike and they are obviously siblings.

 

In the world of Equestria you do not have to look alike to be related. If the various hints described by @Odyssey aren't enough, then it'll be difficult to convince you otherwise.

[Pastel 7,627]

Siblings don't always look alike in MLP:FiM, look at Dinky and her sister:

 

[Princess Oceangem 61]

I have always thought them to be more like best friends/cousins but then again siblings don't always look alike in MLP so...

[UnknownFry 169]

No. The show and other sources keeps hammering down the fact they are sisters.

[Stardust Balance 7,716]

Well other than the Flim Flam brothers, I've yet to see any siblings in the show who look anything alike; Celestia and Luna are evidently not an exception. And personality? Everyone's different in that regard, even royal sisters. 

[Jammo 986]

Twilight and Shining Armor look very different. As do Maud and Pinkie. They actually do have some family resemblance. Body and mane shape... And before anyone says "it's because they're Alicorns" we've seen non-Alicorns with their shape (Fleur de lis) and Twilight still retained her shape even with wings. They are just genetically tall and majestic.

[Cannon and rarity 38]

but 

 

Twilight and Shining Armor look very different. As do Maud and Pinkie. They actually do have some family resemblance. Body and mane shape... And before anyone says "it's because they're Alicorns" we've seen non-Alicorns with their shape (Fleur de lis) and Twilight still retained her shape even with wings. They are just genetically tall and majestic.

you see other ponies in the pie family that look like maud

[MysticShine 529]

They don't have to look alike nor act alike to be siblings. I look nothing like my half brother and sure as hell don't act like him, and we're still related.