In chapter 10, Rainbow Dash accuses Twilight's planned regime as being just as chaotic as Discord's, an idea the author backs up in the comments. However, it can also be argued that Twilight's regime would be the exact opposite of Discord's - a world of total harmony rather than total chaos, but due to the logistics involved, it would be just as bad. Twilight isn't going to become Discord's successor - she's going to become his Foil.
In the first chapter Twilight mentions having experimented on two other ponies before the story began. Only what if those aren't the only ponies she has performed her procedures on?
A few reviewers mentioned a major Fridge Horror when they realized that even after Twilight gains the elements of harmony, she would still need to gain the element of magic that she herself has.
A comment on the fanfic summed up a further realization of Fridge Horror toward the readers...