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New pony theory!
Ok, so Celestia and Luna, apart from being pegacorns, do not look anything alike. They do call each other "sister", but hold on: "sister" can also be an honorific. Like, a female member of some sort of order.
Here's the scoop. Celestia and Luna haven't been doing their jobs forever; Celestia is described as "over a thousand years old" and the oldest pony in equestria, and if Luna had been doing her job since the beginning of time it wouldn't make sense for her to have suddenly flipped out just a thousand years ago. But what if she had just taken the job? What if it was a response to stress she wasn't prepared for?
The theory: The Princesses are not blood siblings, but "sisters" in an order of supreme pony sorceresses. Every thousand years, there's a change: a new pony, probably a unicorn already trained and groomed for it, is turned into a pegacorn and becomes the "younger sister". The former younger sister becomes the older sister, and the previous older sister reaches the end of her lifespan. That's why Luna was able to escape: because Celestia is dying, her powers are running out, and she needed Luna free and fixed in time to replace her. It also explains why Luna, the younger sister, seemed to be more powerful; the older of the pair has their power tied up in various enchantments around Equestria, and Celestia needed to resort to the Elements to imprison Luna. This explains why, despite her power, Luna was only able to pull out illusions and other minor tricks against Twilight and co.; most of her power was tied up in keeping Celestia imprisoned. Celestia's dying also explains why Luna was so suddenly willing to make up with her.
Celestia has sent Twilight to ponyville for a last few experiences as a normal pony, requesting letters from her that she can read and be comforted by in her final days. Twilight will become the new younger sister, and Luna the older.
ALWAYS TWO THERE ARE: THE MASTER, AND THE APPRENTICE.