(1) Why Equestria is not a democracy.
(2) Crazy globe nonwithstanding, Equestria is technically on Earth.
(3) How a non-alicorn can be a prince.
(4) Why most of Celestia's guards are pegasi.
(5) Why winter in Equestria has so many holidays.
Things it does not explain:
(1) How an Alicorn can be a princess.
(2) How Luna knew who Starswirl the Bearded was.
(3) Why nature is so screwy.
...or does it? The (very amusing) play put on in the show is obviously not meant to be taken literally. It's *so* obvious that I can't imagine how it could possibly invalidate any origin story at all that you wanted to make for the show. But if you want to, you can read between the lines and wildly speculate.
The Wendigos were sent by Discord. He was probably also responsible for the initial mistrust, because seriously aside from the fact that they all hated each other (and that the unicorns were probably scammers and/or effectively the church) the original setup was perfectly reasonable.
The mysterious magic of friendship that saved everypony at the end was the creation (or at least the first manifestation) of the Elements of Harmony. Or maybe not... maybe they were already sitting there in the cave which was why it was the last safe place? Maybe the rocks they were fighting over were the elements?
Then, once the elements were revealed, Celestia and Luna came down from the sky to defeat Discord proper, and freeze Equestria in a state of eternal Order. I mean, they're on the flag. Or maybe they were *created* by the elements to defeat Discord? And they're 'no longer connected' because ponies worship them directly now, so they're capable of existing on their own?
...like I said. It didn't explain shit. n.n
But it was possibly the best episode so far. I'm not *sure* about that but it was definately one of my favorites.
(actually, come to think of it, I bet Twilight threw that 'Starswirl the Bearded' name drop in off-script)