Doctor and Twilight work better in terms of story since they're both awesome, and Twilight is more independent than most of the Doctor's companions. She can take care of herself and save him as much as he saves her.
twilicorn: By the way doctor, Celestia was poking around in there and apparently there is video footage of myself and my friends from the past four years of my life stored in there. Would you care to explain yourself?
Twilight my friend, what awaits you is a life more fantastic than anything you could have ever imagined. You will behold events, and peoples, and places on a daily basis that will surpass even your wildest dreams. In one moment you may witness the birth of a star; in the next, an entire galaxy razed to nothing at all. Time itself will bear no more authority over you than that of an empty room. A room where you are free to move about as please, even through the walls and the floor and the ceiling. You will know things before you know them, see the creation of a star system from a speck of dust, and the first time you meet one of your good friends, may be on eve of their death. But don't grieve for them Twilight. Your adventures together. are only just beginning.
"I say, my dear Twilight, want to set off on a adventure of a lifetime across the Universe, seeing all kinds of wonders, making all kinds of friends and battle all kinds of evil for good of all? I assure you it will be positively brilliant!"
"DO I EVER!!"
"Alright then! Into the wild-blue yonder! Allons-y!"