Before Discord rose to madness, he was a young child. He was still a child when his species was wiped from the face of the planet, leaving him to wreak revenge on the country that wronged him.
Before Luna was banished to the moon, she was a beloved princess, sister, and scholar. In her delve to understand magic, she released a monster, and found something leftover, something from the very Creator himself.

An alternate history, starting millennia before Nightmare Moon is banished, and reaching up to season two.
Changes to canon coming later, when we get there.
Not exactly a crossover, but leading into one.