For a while i had an idea involving Twilight and Flash's son. The consept was based on the story resented in the game Kessen 3 which presents the story of Nobunaga Oda in a more virtuos way aswell as a comic made by Yula568.

(Note that i think it could work better as the characters being anthro)
The consept is that Twilight's son(who was born an earth pony) in denied alicornhood and just like in Yula's comic its given to cadance and Shining armor's second daughter aswell as Twilight's older and younger daughter.

The son ofcourse lashes out and coments he was denied for being a stallion which gets him a repremation of his mother and the other princesses, this causes him to flee equestria and go beyond know terretory.

On his travels he is taught by an old master and hermit (who could infact be a hidden starswhirl or other character), diferent sciences amounst other things. After leaving he gains allies goes to battles and unifies the warring land beyond equestria and he becomes emperor.

Later coming in contact with equestria as said country comes to form an alliance.

For more ideas on the story see this:

Basacly her son would be a pony version of Nobunaga.