Minami-ke/WMG

Chiaki Minami is a savant
Chiaki is exceptionally brilliant in school. She can even spontaneously answer the following question, which was asked by Kana in episode 3 of the first series:

"Kana: In May of a certain year, there are 4 Tuesdays and 4 Fridays; What day is the 5th of May that year?

Chiaki: Wednesday."

By looking at a calendar and doing some computations, you can determine that this answer is correct; but answering that kind of question that quickly without a calendar, paper, or a calculator is not something normal people can do. This ability is, however, a typical savant trait.

Also, Chiaki has weak interpersonal skills and isn't able to adequately express emotions outwardly. This is another typical trait of savants.

Chiaki is Yuki Nagato
Both characters are robotically bereft of facial expressions, both are incredibly bookish, and both are voiced by Minori Chihara. The problem in this theory arises when you consider that Yuki is a Badass Bookworm, while Chiaki is probably not that Badass at all. Also. Yuki is not the type of girl you could call a deadpan snarker.
 * Unless...

Minami-ke is set in a parallel world where cleft lips are the norm.
Why else would everybody have those teardrop mouths?
 * So is Konata actually from that world? That raises even more questions, of course.

The sisters are actually the three Norns from Ah! My Goddess in disguise as mortals.
Belldandy is Haruka, Urd is Kana, and Skuld is Chiaki. Before they could take their full divine positions (that is, before being granted any divine powers), they were obligated to live as three mortal girls in order to get to know humanity. This explains why they're living on their own without any parents.

Chiaki gave life to Luna Child.
Cleft lips, two sisters, perpetually mad expression. Obviously when she was a little girl, she thought up the fairy, and when she stopped believing in it, she went to Gensokyo.

Kana is a can containing some sealed evil.
Poking her on the butt briefly weakens the seal, much to the dismay of the audience.

"I AM BOSS" is actually a case of Surprisingly Good English.
The word 'boss' is actually being used in the adjective slang sense where it means 'great' or 'awesome', e.g. "Oh, man, that is boss!"