Here's an idea for a comic, another TNG reference. A bit more serious, but it could be interesting: what if Twilight dies by some means, and runs into Discord, who claims to be Fausticorn (Pony equivalent to God) or something along those lines. Like with Picard, Twi is shown what her life would be like if she never left Canterlot, never met her friends, and never became the Bearer of Magic. Might have to leave out the Nightmare Moon thing or the world would be covered in eternal night without anypony around to stop her. Either that or someone else came the Bearer of Magic.
I hope Discord does make a comeback in the series. Even if they can't get John de Lancie again, they could get someone who at least sounds similar. I want him to either come back as a a villain again or tries to become a friend like in this comic.
I can actually see that happening and he could probably teach Twilight about the history before his rule over Equestria. And for all those shippers, he could have a crush on Celestia. The idea of that kinda scared me at first but now it seems interesting.